% Encoding: UTF-8


@String { ARB       = {Annu. Rev. Biochem.} }
@String { BBA       = {Biochim. Biophys. Act.} }
@String { BPJ       = {Biophys. J.} }
@String { BullAMS   = {Bull. Am. Mat. Soc.} }
@String { CPL       = {Chem. Phys. Lipids} }
@String { JACS      = {J. Am. Phys. Soc.} }
@String { JCOMPCHEM = {J. Comp. Chem.} }
@String { JCP       = {J. Chem. Phys.} }
@String { JMB       = {J. Mol. Biol.} }
@String { JPCA      = {J. Phys. Chem. A} }
@String { JPCB      = {J. Phys. Chem. B} }
@String { NANO      = {Nano. Lett.} }
@String { PNAS      = {Proc. Natl. Acad. Sci. USA} }
@String { PRE       = {Phys. Rev. E} }
@String { PS        = {Prot. Sci.} }
@String { PTRSA     = {Phil. Trans. R. Soc. A} }
@String { ST        = {Structure} }

@Article{Abad-Zapatero1980,
  Title                    = {Structure of southern bean mosaic virus at 2.8 $\mbox{\AA}$ resolution},
  Author                   = {Abad-Zapatero,C. and Abdel-Meguid,S.S. and Johnson,J.E. and Leslie,A.G.W. and Rayment,I. and Rossmann,M.G. and Suck,D. and Tsukihara,T.},
  Journal                  = {Nature},
  Year                     = {1980},
  Pages                    = {33--39},
  Volume                   = {286},

  File                     = {Abad-Zapatero1980.pdf:pdfs/Abad-Zapatero1980.pdf:PDF},
  Owner                    = {ranjan},
  Timestamp                = {2009.08.19}
}

@Article{Abascal2005,
  Title                    = {ProtTest: selection of best-fit models of protein evolution.},
  Author                   = {Abascal, Federico and Zardoya, Rafael and Posada, David},
  Journal                  = {Bioinformatics},
  Year                     = {2005},

  Month                    = {May},
  Number                   = {9},
  Pages                    = {2104--2105},
  Volume                   = {21},

  Abstract                 = {SUMMARY: Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment. AVAILABILITY: ProtTest is available under the GNU license from http://darwin.uvigo.es},
  Keywords                 = {Algorithms; Amino Acid Sequence; Amino Acid Substitution, genetics; Amino Acids, chemistry/genetics; Computer Graphics; Computer Simulation; DNA Mutational Analysis, methods; Evolution, Molecular; Humans; Internet; Models, Genetic; Models, Molecular; Molecular Sequence Data; Mutagenesis, Site-Directed, genetics; Phylogeny; Proteins, chemistry/genetics; Sequence Analysis, Protein, methods; Software; Structure-Activity Relationship; User-Computer Interface},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {bti263},
  Pmid                     = {15647292},
  Timestamp                = {2012.09.10}
}

@Article{Abkevich1997,
  Title                    = {Computer simulations of prebiotic evolution.},
  Author                   = {V. I. Abkevich and A. M. Gutin and E. I. Shakhnovich},
  Journal                  = {Pac Symp Biocomput},
  Year                     = {1997},
  Pages                    = {27--38},

  Abstract                 = {This paper is a review of our previous work on the field of possible ways of prebiotic evolution. We propose an algorithm providing sequences of model proteins with rapid folding into a given native conformation. Thermodynamical analysis shows that the increase in speed is matched by an increase in stability: the evolved sequences are much more stable in their native conformation than the initial random sequence. We discuss a possible origin of the first biopolymers, having stable unique structure. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact in order to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences of model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structure of first biopolymers could have evolved as a 
side effect of a nonspecific physico-chemical factors acting at the prebiotic stage of evolution.},
  File                     = {Abkevich1997.pdf:pdfs/Abkevich1997.pdf:PDF},
  Institution              = {Harvard University, Department of Chemistry, Cambridge, MA 02138, USA.},
  Keywords                 = {Algorithms; Biogenesis; Computer Simulation; Evolution; Models, Biological; Models, Molecular; Mutation; Protein Conformation; Proteins, chemistry/genetics; Random Allocation; Software; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {9390277},
  Timestamp                = {2009.12.05}
}

@Article{Abkevich1996,
  Title                    = {How the first biopolymers could have evolved.},
  Author                   = {V. I. Abkevich and A. M. Gutin and E. I. Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1996},

  Month                    = {Jan},
  Number                   = {2},
  Pages                    = {839--844},
  Volume                   = {93},

  Abstract                 = {In this work, we discuss a possible origin of the first biopolymers with stable unique structures. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences for model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structures of first biopolymers could have evolved as a side effect of nonspecific physicochemical factors acting at the prebiotic stage of evolution.},
  File                     = {Abkevich1996.pdf:pdfs/Abkevich1996.pdf:PDF},
  Institution              = {Harvard University, Department of Chemistry, Cambridge, MA 02138, USA.},
  Keywords                 = {Algorithms; Biogenesis; Biopolymers; Evolution; Peptides, chemistry; Protein Folding},
  Owner                    = {ranjan},
  Pmid                     = {8570645},
  Timestamp                = {2009.12.05}
}

@Article{Abkevich1995,
  Title                    = {Impact of local and non-local interactions on thermodynamics and kinetics of protein folding.},
  Author                   = {V. I. Abkevich and A. M. Gutin and E. I. Shakhnovich},
  Journal                  = {J Mol Biol},
  Year                     = {1995},

  Month                    = {Sep},
  Number                   = {4},
  Pages                    = {460--471},
  Volume                   = {252},

  Abstract                 = {To address the question of how the geometry of a protein's native conformation affects its folding and stability, we studied three model 36-mers on a cubic lattice. The native structure of one of these model 36-mers consisted mostly of local contacts, while that of a second consisted mostly of non-local contacts. The third native structure had a typical compact native conformation, and served as our reference. For each protein, the amino acid sequence was designed to have a pronounced energy minimum at its native conformation. We observed dramatic differences in folding, dependent on the presence or absence of non-local contacts. For the proteins with a typical large number of non-local contacts, the folding transition was all-or-none, whereas for the one with mostly local contacts, it was not. Although the maximum rate of folding was similar for all three proteins, we found that under conditions at which each native conformation was stable, the structure with mostly non-local 
contacts folded two orders of magnitude faster than the one with mostly local contacts. The statistical analysis of protein structure agrees fully with the implications of the theory. We discuss the importance of cooperativity in protein folding for its stability.},
  File                     = {Abkevich1995.pdf:pdfs/Abkevich1995.pdf:PDF},
  Institution              = {Harvard University, Department of Chemistry, Cambridge, MA 02138, USA.},
  Keywords                 = {Amino Acid Sequence; Computer Simulation; Kinetics; Models, Chemical; Molecular Sequence Data; Protein Conformation; Protein Folding; Proteins, chemistry; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(85)70511-6},
  Pmid                     = {7563065},
  Timestamp                = {2010.01.18}
}

@Article{Adami2006,
  Title                    = {Digital genetics: unravelling the genetic basis of evolution.},
  Author                   = {Christoph Adami},
  Journal                  = {Nat Rev Genet},
  Year                     = {2006},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {109--118},
  Volume                   = {7},

  Abstract                 = {Digital genetics, or the genetics of digital organisms, is a new field of research that has become possible as a result of the remarkable power of evolution experiments that use computers. Self-replicating strands of computer code that inhabit specially prepared computers can mutate, evolve and adapt to their environment. Digital organisms make it easy to conduct repeatable, controlled experiments, which have a perfect genetic 'fossil record'. This allows researchers to address fundamental questions about the genetic basis of the evolution of complexity, genome organization, robustness and evolvability, and to test the consequences of mutations, including their interaction and recombination, on the fate of populations and lineages.},
  Institution              = {Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711, USA. adami@kgi.edu},
  Keywords                 = {Computational Biology, methods; Computer Simulation; Evolution, Molecular; Genetics, Population, trends; Models, Genetic},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nrg1771},
  Pmid                     = {16418746},
  Timestamp                = {2011.07.09}
}

@Article{Adami2006a,
  Title                    = {Reducible complexity},
  Author                   = {Adami, Christoph},
  Journal                  = {Science},
  Year                     = {2006},
  Number                   = {5770},
  Pages                    = {61--63},
  Volume                   = {312},

  Owner                    = {ranjan},
  Publisher                = {American Association for the Advancement of Science},
  Timestamp                = {2013.12.03}
}

@Article{Adami2002,
  Title                    = {What is complexity?},
  Author                   = {Christoph Adami},
  Journal                  = {Bioessays},
  Year                     = {2002},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {1085--1094},
  Volume                   = {24},

  Abstract                 = {Arguments for or against a trend in the evolution of complexity are weakened by the lack of an unambiguous definition of complexity. Such definitions abound for both dynamical systems and biological organisms, but have drawbacks of either a conceptual or a practical nature. Physical complexity, a measure based on automata theory and information theory, is a simple and intuitive measure of the amount of information that an organism stores, in its genome, about the environment in which it evolves. It is argued that physical complexity must increase in molecular evolution of asexual organisms in a single niche if the environment does not change, due to natural selection. It is possible that complexity decreases in co-evolving systems as well as at high mutation rates, in sexual populations, and in time-dependent landscapes. However, it is reasoned that these factors usually help, rather than hinder, the evolution of complexity, and that a theory of physical complexity for co-
evolving species will reveal an overall trend towards higher complexity in biological evolution.},
  Institution              = {Digital Life Laboratory 136-93, California Institute of Technology, Pasadena 91109, USA. adami@caltech.edu},
  Keywords                 = {Animals; Biological Evolution; Ecosystem; Entropy; Humans; Information Theory; Models, Biological; Models, Statistical; Time Factors},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {12447974},
  Timestamp                = {2011.07.09}
}

@Article{Adami2000,
  Title                    = {Evolution of biological complexity.},
  Author                   = {C. Adami and C. Ofria and T. C. Collier},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2000},

  Month                    = {Apr},
  Number                   = {9},
  Pages                    = {4463--4468},
  Volume                   = {97},

  Abstract                 = {To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural ``Maxwell Demon,'' within a fixed environment, genomic complexity is forced to increase.},
  Institution              = {Kellogg Radiation Laboratory 106-38, California Institute of Technology, Pasadena, CA 91125, USA. adami@krl.caltech.edu},
  Keywords                 = {Biological Evolution; Biology, methods; DNA, genetics; Entropy; Evolution, Molecular; Fossils; Genome; Information Theory; Models, Genetic; Models, Statistical},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {97/9/4463},
  Pmid                     = {10781045},
  Timestamp                = {2011.07.09}
}

@Article{Adzhubei1993,
  Title                    = {Left-handed polyproline II helices commonly occur in globular proteins},
  Author                   = {Adzhubei, Alexei A and Sternberg, Michael JE},
  Journal                  = {Journal of molecular biology},
  Year                     = {1993},
  Number                   = {2},
  Pages                    = {472--493},
  Volume                   = {229},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2016.06.06}
}

@Article{Aguado-Llera2013,
  Title                    = {Deciphering the Binding between Nupr1 and MSL1 and Their DNA-Repairing Activity.},
  Author                   = {Aguado-Llera, David and Hamidi, Tewfik and Doménech, Rosa and Pantoja-Uceda, David and Gironella, Meritxell and Santoro, Jorge and Velázquez-Campoy, Adrián and Neira, José L. and Iovanna, Juan L.},
  Journal                  = {PLoS One},
  Year                     = {2013},
  Number                   = {10},
  Pages                    = {e78101},
  Volume                   = {8},

  Abstract                 = {The stress protein Nupr1 is a highly basic, multifunctional, intrinsically disordered protein (IDP). MSL1 is a histone acetyl transferase-associated protein, known to intervene in the dosage compensation complex (DCC). In this work, we show that both Nupr1 and MSL1 proteins were recruited and formed a complex into the nucleus in response to DNA-damage, which was essential for cell survival in reply to cisplatin damage. We studied the interaction of Nupr1 and MSL1, and their binding affinities to DNA by spectroscopic and biophysical methods. The MSL1 bound to Nupr1, with a moderate affinity (2.8 µM) in an entropically-driven process. MSL1 did not bind to non-damaged DNA, but it bound to chemically-damaged-DNA with a moderate affinity (1.2 µM) also in an entropically-driven process. The Nupr1 protein bound to chemically-damaged-DNA with a slightly larger affinity (0.4 µM), but in an enthalpically-driven process. Nupr1 showed different interacting regions in the formed complexes 
with Nupr1 or DNA; however, they were always disordered ("fuzzy"), as shown by NMR. These results underline a stochastic description of the functionality of the Nupr1 and its other interacting partners.},
  Doi                      = {10.1371/journal.pone.0078101},
  Institution              = {Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain.},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {PONE-D-13-29113},
  Pmid                     = {24205110},
  Timestamp                = {2013.12.14}
}

@Article{Aharoni2004,
  Title                    = {The `evolvability' of promiscuous protein functions},
  Author                   = {Aharoni, Amir and Gaidukov, Leonid and Khersonsky, Olga and Gould, Stephen McQ and Roodveldt, Cintia and Tawfik, Dan S},
  Journal                  = {Nature genetics},
  Year                     = {2004},
  Number                   = {1},
  Pages                    = {73--76},
  Volume                   = {37},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2013.11.19}
}

@Article{Alberts2002,
  Title                    = {Molecular Biology of the Cell. New York: Garland Science; 2002},
  Author                   = {Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Raff, Martin and Roberts, Keith and Walter, Peter},
  Journal                  = {Classic textbook now in its 5th Edition},
  Year                     = {2002},

  Owner                    = {ranjan},
  Timestamp                = {2015.09.09}
}

@Article{Alexander1932,
  Title                    = {Some intracellular aspects of life and disease},
  Author                   = {Alexander, Jerome},
  Journal                  = {Protoplasma},
  Year                     = {1932},
  Number                   = {1},
  Pages                    = {296--306},
  Volume                   = {14},

  Owner                    = {ranjan},
  Publisher                = {Springer},
  Timestamp                = {2013.12.03}
}

@Article{Alexander2009,
  Title                    = {A minimal sequence code for switching protein structure and function.},
  Author                   = {Alexander, Patrick A. and He, Yanan and Chen, Yihong and Orban, John and Bryan, Philip N.},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2009},

  Month                    = {Dec},
  Number                   = {50},
  Pages                    = {21149--21154},
  Volume                   = {106},

  Abstract                 = {We present here a structural and mechanistic description of how a protein changes its fold and function, mutation by mutation. Our approach was to create 2 proteins that (i) are stably folded into 2 different folds, (ii) have 2 different functions, and (iii) are very similar in sequence. In this simplified sequence space we explore the mutational path from one fold to another. We show that an IgG-binding, 4beta+alpha fold can be transformed into an albumin-binding, 3-alpha fold via a mutational pathway in which neither function nor native structure is completely lost. The stabilities of all mutants along the pathway are evaluated, key high-resolution structures are determined by NMR, and an explanation of the switching mechanism is provided. We show that the conformational switch from 4beta+alpha to 3-alpha structure can occur via a single amino acid substitution. On one side of the switch point, the 4beta+alpha fold is >90\% populated (pH 7.2, 20 degrees C). A single mutation 
switches the conformation to the 3-alpha fold, which is >90\% populated (pH 7.2, 20 degrees C). We further show that a bifunctional protein exists at the switch point with affinity for both IgG and albumin.},
  Institution              = {Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA.},
  Keywords                 = {Humans; Immunoglobulin G; Magnetic Resonance Spectroscopy; Mutagenesis, Site-Directed; Mutation; Protein Conformation; Protein Engineering, methods; Protein Folding; Protein Stability; Recombinant Fusion Proteins, chemistry/genetics/physiology; Serum Albumin; Subtilisin, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {0906408106},
  Pmid                     = {19923431},
  Timestamp                = {2013.06.13}
}

@Article{Alexander2007,
  Title                    = {The design and characterization of two proteins with 88% sequence identity but different structure and function.},
  Author                   = {Alexander, Patrick A. and He, Yanan and Chen, Yihong and Orban, John and Bryan, Philip N.},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2007},

  Month                    = {Jul},
  Number                   = {29},
  Pages                    = {11963--11968},
  Volume                   = {104},

  Abstract                 = {To identify a simplified code for conformational switching, we have redesigned two natural proteins to have 88\% sequence identity but different tertiary structures: a 3-alpha helix fold and an alpha/beta fold. We describe the design of these homologous heteromorphic proteins, their structural properties as determined by NMR, their conformational stabilities, and their affinities for their respective ligands: IgG and serum albumin. Each of these proteins is completely folded at 25 degrees C, is monomeric, and retains the native binding activity. The complete binding epitope for both ligands is encoded within each of the proteins. The IgG-binding epitope is functional only in the alpha/beta fold, and the albumin-binding epitope is functional only in the 3-alpha fold. These results demonstrate that two monomeric folds and two different functions can be encoded with only 12\% of the amino acids in a protein (7 of 56). The fact that 49 aa in these proteins are compatible with both 
folds shows that the essential information determining a fold can be highly concentrated in a few amino acids and that a very limited subset of interactions in the protein can tip the balance from one monomer fold to another. This delicate balance helps explain why protein structure prediction is so challenging. Furthermore, because a few mutations can result in both new conformation and new function, the evolution of new folds driven by natural selection for alternative functions may be much more probable than previously recognized.},
  Institution              = {Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA.},
  Keywords                 = {Amino Acid Sequence; Bacterial Proteins, chemistry/metabolism; Binding Sites; Circular Dichroism; Epitopes, chemistry; Humans; Molecular Sequence Data; Mutant Proteins, chemistry/metabolism; Mutation, genetics; Nuclear Magnetic Resonance, Biomolecular; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Sequence Homology, Amino Acid; Serum Albumin, metabolism; Streptococcus, chemistry; Structure-Activity Relationship; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {0700922104},
  Pmid                     = {17609385},
  Timestamp                = {2013.06.13}
}

@Book{Allen1989,
  Title                    = {Computer Simulation of Liquids},
  Author                   = {M. P. Allen and D. J. Tildesley},
  Publisher                = {Oxford University Press, USA},
  Year                     = {1989},

  Owner                    = {ranjan},
  Timestamp                = {2012.07.14}
}

@Article{Altschul1997,
  Title                    = {Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.},
  Author                   = {S. F. Altschul and T. L. Madden and A. A. Sch\"{a}ffer and J. Zhang and Z. Zhang and W. Miller and D. J. Lipman},
  Journal                  = {Nucleic Acids Res},
  Year                     = {1997},

  Month                    = {Sep},
  Number                   = {17},
  Pages                    = {3389--3402},
  Volume                   = {25},

  Abstract                 = {The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence 
similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.},
  Institution              = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. altschul@ncbi.nlm.nih.gov},
  Keywords                 = {Algorithms; Amino Acid Sequence; Animals; DNA, chemistry; Databases, Factual; Humans; Molecular Sequence Data; Proteins, chemistry; Sequence Alignment; Software},
  Owner                    = {ranjan},
  Pii                      = {gka562},
  Pmid                     = {9254694},
  Timestamp                = {2010.05.02}
}

@Article{Alvarez2009,
  Title                    = {Atmospheric collapse in self-avoiding walks: a numerical study using GARM},
  Author                   = {Alvarez, J and Gara, M and van Rensburg, EJ Janse and Rechnitzer, A},
  Journal                  = {Journal of Statistical Mechanics: Theory and Experiment},
  Year                     = {2009},
  Number                   = {12},
  Pages                    = {P12005},
  Volume                   = {2009},

  Owner                    = {ranjan},
  Publisher                = {IOP Publishing},
  Timestamp                = {2014.08.31}
}

@Article{Alvarez-Valin2004,
  Title                    = {Inaccurate reconstruction of ancestral GC levels creates a ``vanishing isochores'' effect.},
  Author                   = {Fernando Alvarez-Valin and Oliver Clay and St?phane Cruveiller and Giorgio Bernardi},
  Journal                  = {Mol Phylogenet Evol},
  Year                     = {2004},

  Month                    = {May},
  Number                   = {2},
  Pages                    = {788--793},
  Volume                   = {31},

  Abstract                 = {It has recently been proposed, based on an analysis of orthologous gene sequences from closely related species, that GC-rich regions of primate and cetartiodactyl genomes are becoming GC-poorer, i.e., that GC-rich isochores are now vanishing in these lineages. We review an artefact of parsimony-based ancestor reconstruction in GC-rich DNA, and show that its magnitude explains the apparent vanishing of the GC-richest regions in cetartiodactyls, even if they are in fact at compositional equilibrium. The presently available data do not allow the disequilibrium hypothesis to be entirely ruled out in primates, yet, as we argue here, second-order artefacts can accumulate. They are therefore likely to explain many if not all of the observations, rendering unnecessary the general hypothesis of vanishing GC-rich isochores in mammals.},
  Institution              = {Secci?n Biomatem?tica, Facultad de Ciencias, Montevideo 11400, Uruguay.},
  Keywords                 = {Animals; Artifacts; Base Composition; GC Rich Sequence; Interspersed Repetitive Sequences; Isochores, genetics; Linkage Disequilibrium; Mammals, genetics; Primates, genetics; Sequence Analysis, DNA},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S1055790304000569},
  Pmid                     = {15062812},
  Timestamp                = {2011.09.15}
}

@Article{Alvizo2007,
  Title                    = {Computational protein design promises to revolutionize protein engineering.},
  Author                   = {Oscar Alvizo and Benjamin D Allen and Stephen L Mayo},
  Journal                  = {Biotechniques},
  Year                     = {2007},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {31, 33, 35 passim},
  Volume                   = {42},

  Abstract                 = {Natural evolution has produced an astounding array of proteins that perform the physical and chemical functions required for life on Earth. Although proteins can be reengineered to provide altered or novel functions, the utility of this approach is limited by the difficulty of identifying protein sequences that display the desired properties. Recently, advances in the field of computational protein design (CPD) have shown that molecular simulation can help to predict sequences with new and improved functions. In the past few years, CPD has been used to design protein variants with optimized specificity of binding to DNA, small molecules, peptides, and other proteins. Initial successes in enzyme design highlight CPD's unique ability to design function de novo. The use of CPD for the engineering of potential therapeutic agents has demonstrated its strength in real-life applications.},
  Institution              = {Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, CA, USA.},
  Keywords                 = {Computer Simulation; Models, Molecular; Protein Conformation; Protein Engineering, methods},
  Owner                    = {ranjan},
  Pii                      = {000112336},
  Pmid                     = {17269482},
  Timestamp                = {2010.12.29}
}

@Article{Amadei1993,
  Title                    = {Essential dynamics of proteins.},
  Author                   = {Amadei, A. and Linssen, A. B. and Berendsen, H. J.},
  Journal                  = {Proteins},
  Year                     = {1993},

  Month                    = {Dec},
  Number                   = {4},
  Pages                    = {412--425},
  Volume                   = {17},

  Abstract                 = {Analysis of extended molecular dynamics (MD) simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the configurational space into two subspaces: (1) an "essential" subspace containing only a few degrees of freedom in which anharmonic motion occurs that comprises most of the positional fluctuations; and (2) the remaining space in which the motion has a narrow Gaussian distribution and which can be considered as "physically constrained." If overall translation and rotation are eliminated, the two spaces can be constructed by a simple linear transformation in Cartesian coordinate space, which remains valid over several hundred picoseconds. The transformation follows from the covariance matrix of the positional deviations. The essential degrees of freedom seem to describe motions which are relevant for the function of the protein, while the physically constrained subspace merely describes irrelevant local fluctuations. The near-constraint 
behavior of the latter subspace allows the separation of equations of motion and promises the possibility of investigating independently the essential space and performing dynamic simulations only in this reduced space.},
  Doi                      = {10.1002/prot.340170408},
  Institution              = {Department of Biophysical Chemistry, University of Groningen, The Netherlands.},
  Keywords                 = {Animals; Chickens; Egg White; Models, Chemical; Models, Theoretical; Muramidase, chemistry/physiology},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {8108382},
  Timestamp                = {2014.02.08}
}

@Article{Anders1989,
  Title                    = {Pre-biotic organic matter from comets and asteroids.},
  Author                   = {E. Anders},
  Journal                  = {Nature},
  Year                     = {1989},

  Month                    = {Nov},
  Number                   = {6247},
  Pages                    = {255--257},
  Volume                   = {342},

  Abstract                 = {Several authors have suggested that comets or carbonaceous asteroids contributed large amounts of organic matter to the primitive Earth, and thus possibly played a vital role in the origin of life. But organic matter cannot survive the extremely high temperatures (>10(4) K) reached on impact, which atomize the projectile and break all chemical bonds. Only fragments small enough to be gently decelerated by the atmosphere--principally meteors of 10(-12)-10(-6) g--can deliver their organic matter intact. The amount of such 'soft-landed' organic carbon can be estimated from data for the infall rate of meteoritic matter. At present rates, only approximately 0.006 g cm-2 intact organic carbon would accumulate in 10(8) yr, but at the higher rates of approximately 4 x 10(9) yr ago, about 20 g cm-2 may have accumulated in the few hundred million years between the last cataclysmic impact and the beginning of life. It may have included some biologically important compounds that did not 
form by abiotic synthesis on Earth.},
  File                     = {Anders1989.pdf:pdfs/Anders1989.pdf:PDF},
  Institution              = {Department of Chemistry, University of Chicago, Illinois 60637-1433, USA.},
  Keywords                 = {Atmosphere; Biogenesis; Carbon, analysis/chemistry; Earth (Planet); Evolution, Chemical; Extraterrestrial Environment; Hot Temperature; Hydrogen; Meteoroids; Minor Planets; Nitrogen},
  Owner                    = {ranjan},
  Pmid                     = {11536617},
  Timestamp                = {2009.09.21}
}

@InProceedings{Anderson1995,
  Title                    = {Data and computation transformations for multiprocessors},
  Author                   = {Anderson, Jennifer M and Amarasinghe, Saman P and Lam, Monica S},
  Booktitle                = {ACM SIGPLAN Notices},
  Year                     = {1995},
  Number                   = {8},
  Organization             = {ACM},
  Pages                    = {166--178},
  Volume                   = {30},

  Owner                    = {ranjan},
  Timestamp                = {2015.09.04}
}

@Article{Anfinsen1961,
  Title                    = {Studies on the reduction and re-formation of protein disulfide bonds.},
  Author                   = {Anfinsen, C. B. and Haber, E.},
  Journal                  = {J Biol Chem},
  Year                     = {1961},

  Month                    = {May},
  Pages                    = {1361--1363},
  Volume                   = {236},

  Keywords                 = {Proteins, chemistry; Ribonucleases, chemistry; Sulfides, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {13683523},
  Timestamp                = {2013.11.12}
}

@Article{Arbiza2011,
  Title                    = {Genome-wide heterogeneity of nucleotide substitution model fit.},
  Author                   = {Arbiza, Leonardo and Patricio, Mateus and Dopazo, Hern?n and Posada, David},
  Journal                  = {Genome Biol Evol},
  Year                     = {2011},
  Pages                    = {896--908},
  Volume                   = {3},

  Abstract                 = {At a genomic scale, the patterns that have shaped molecular evolution are believed to be largely heterogeneous. Consequently, comparative analyses should use appropriate probabilistic substitution models that capture the main features under which different genomic regions have evolved. While efforts have concentrated in the development and understanding of model selection techniques, no descriptions of overall relative substitution model fit at the genome level have been reported. Here, we provide a characterization of best-fit substitution models across three genomic data sets including coding regions from mammals, vertebrates, and Drosophila (24,000 alignments). According to the Akaike Information Criterion (AIC), 82 of 88 models considered were selected as best-fit models at least in one occasion, although with very different frequencies. Most parameter estimates also varied broadly among genes. Patterns found for vertebrates and Drosophila were quite similar and often more 
complex than those found in mammals. Phylogenetic trees derived from models in the 95\% confidence interval set showed much less variance and were significantly closer to the tree estimated under the best-fit model than trees derived from models outside this interval. Although alternative criteria selected simpler models than the AIC, they suggested similar patterns. All together our results show that at a genomic scale, different gene alignments for the same set of taxa are best explained by a large variety of different substitution models and that model choice has implications on different parameter estimates including the inferred phylogenetic trees. After taking into account the differences related to sample size, our results suggest a noticeable diversity in the underlying evolutionary process. All together, we conclude that the use of model selection techniques is important to obtain consistent phylogenetic estimates from real data at a genomic scale.},
  Institution              = {Department of Biochemistry, Genetics, and Immunology, University of Vigo, Vigo, Spain.},
  Keywords                 = {Animals; Drosophila, genetics; Evolution, Molecular; Genome; Mammals, genetics; Models, Genetic; Mutation; Nucleotides, genetics; Open Reading Frames, genetics; Phylogeny; Sequence Alignment; Vertebrates, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {evr080},
  Pmid                     = {21824869},
  Timestamp                = {2012.09.10}
}

@Article{Arenas2010,
  Title                    = {Coalescent simulation of intracodon recombination.},
  Author                   = {Arenas, Miguel and Posada, David},
  Journal                  = {Genetics},
  Year                     = {2010},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {429--437},
  Volume                   = {184},

  Abstract                 = {The coalescent with recombination is a very useful tool in molecular population genetics. Under this framework, genealogies often represent the evolution of the substitution unit, and because of this, the few coalescent algorithms implemented for the simulation of coding sequences force recombination to occur only between codons. However, it is clear that recombination is expected to occur most often within codons. Here we have developed an algorithm that can evolve coding sequences under an ancestral recombination graph that represents the genealogies at each nucleotide site, thereby allowing for intracodon recombination. The algorithm is a modification of Hudson's coalescent in which, in addition to keeping track of events occurring in the ancestral material that reaches the sample, we need to keep track of events occurring in ancestral material that does not reach the sample but that is produced by intracodon recombination. We are able to show that at typical substitution 
rates the number of nonsynonymous changes induced by intracodon recombination is small and that intracodon recombination does not generally result in inflated estimates of the overall nonsynonymous/synonymous substitution ratio (omega). On the other hand, recombination can bias the estimation of omega at particular codons, resulting in apparent rate variation among sites and in the spurious identification of positively selected sites. Importantly, in this case, allowing for variable synonymous rates across sites greatly reduces the false-positive rate and recovers statistical power. Finally, coalescent simulations with intracodon recombination could be used to better represent the evolution of nuclear coding genes or fast-evolving pathogens such as HIV-1.We have implemented this algorithm in a computer program called NetRecodon, freely available at http://darwin.uvigo.es.},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {genetics.109.109736},
  Pmid                     = {19933876},
  Timestamp                = {2012.07.09}
}

@Article{Arenas2010a,
  Title                    = {The effect of recombination on the reconstruction of ancestral sequences.},
  Author                   = {Arenas, Miguel and Posada, David},
  Journal                  = {Genetics},
  Year                     = {2010},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {1133--1139},
  Volume                   = {184},

  Abstract                 = {While a variety of methods exist to reconstruct ancestral sequences, all of them assume that a single phylogeny underlies all the positions in the alignment and therefore that recombination has not taken place. Using computer simulations we show that recombination can severely bias ancestral sequence reconstruction (ASR), and quantify this effect. If recombination is ignored, the ancestral sequences recovered can be quite distinct from the grand most recent common ancestor (GMRCA) of the sample and better resemble the concatenate of partial most recent common ancestors (MRCAs) at each recombination fragment. When independent phylogenetic trees are assumed for the different recombinant segments, the estimation of the fragment MRCAs improves significantly. Importantly, we show that recombination can change the biological predictions derived from ASRs carried out with real data. Given that recombination is widespread on nuclear genes and in particular in RNA viruses and some 
bacteria, the reconstruction of ancestral sequences in these cases should consider the potential impact of recombination and ideally be carried out using approaches that accommodate recombination.},
  Keywords                 = {Base Sequence; Computer Simulation; Genetic Variation; Models, Genetic; Phylogeny; Recombination, Genetic, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {genetics.109.113423},
  Pmid                     = {20124027},
  Timestamp                = {2012.09.10}
}

@Article{Arkhipov2006,
  Title                    = {Stability and dynamics of virus capsids described by coarse-grained modeling.},
  Author                   = {Arkhipov, A. and Freddolino, P.L. and Schulten, K.},
  Journal                  = {Structure.},
  Year                     = {2006},
  Number                   = {12},
  Pages                    = {1767-1777},
  Volume                   = {14},

  File                     = {:pdfs/Arkhipov2006.pdf:PDF},
  Owner                    = {ranjan}
}

@Article{Armen2004,
  Title                    = {Pauling and Corey's $\alpha$-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease},
  Author                   = {Armen, Roger S and DeMarco, Mari L and Alonso, Darwin OV and Daggett, Valerie},
  Journal                  = {Proceedings of the National Academy of Sciences of the United States of America},
  Year                     = {2004},
  Number                   = {32},
  Pages                    = {11622--11627},
  Volume                   = {101},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2015.11.15}
}

@Article{Arndt2007,
  Title                    = {Reconstruction of ancestral nucleotide sequences and estimation of substitution frequencies in a star phylogeny.},
  Author                   = {Peter F Arndt},
  Journal                  = {Gene},
  Year                     = {2007},

  Month                    = {Apr},
  Number                   = {1-2},
  Pages                    = {75--83},
  Volume                   = {390},

  Abstract                 = {Maximum likelihood phylogeny reconstruction methods are widely used in uncovering and assessing the evolutionary history and relationships of natural systems. However, several simplifying assumptions commonly made in this analysis limit the explanatory power of the results obtained. We present an algorithm that performs the phylogenetic analysis without making the common assumptions for sequence data from at least three leaf nodes in a star phylogeny. In particular, the underlying nucleotide substitution model does not have to be reversible and may include neighbor-dependent processes like the CpG methylation deamination process (CpG-effect). The base composition of the sequences at the external nodes and the one of the ancestral sequence may be different from each other and they do not have to be stationary state distributions of the corresponding substitution model. The algorithm is able to reconstruct the ancestral base composition and accurately estimate substitution 
frequencies in the branches of the star phylogeny. Extensive tests on simulated data validate the very favorable performance of the algorithm. As an application we present the analysis of aligned genomic sequences from human, mouse, and dog. Different substitution pattern can be observed in the three lineages.},
  Institution              = {Max Planck Institute for Molecular Genetics, Ihnestr. 63, 14195 Berlin, Germany. arndt@molgen.mpg.de},
  Keywords                 = {Algorithms; Animals; Base Composition; CpG Islands; DNA, genetics; Dogs; Evolution, Molecular; Humans; Likelihood Functions; Mice; Models, Genetic; Monte Carlo Method; Phylogeny; Sequence Alignment},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0378-1119(06)00714-1},
  Pmid                     = {17223282},
  Timestamp                = {2011.09.15}
}

@Article{Ashwin2013,
  Title                    = {Inherent Structure Landscape Connection between Liquids, Granular Materials, and the Jamming Phase Diagram},
  Author                   = {Ashwin, SS and Yamchi, Mahdi Zaeifi and Bowles, Richard K},
  Journal                  = {Physical review letters},
  Year                     = {2013},
  Number                   = {14},
  Pages                    = {145701},
  Volume                   = {110},

  Owner                    = {ranjan},
  Publisher                = {APS},
  Timestamp                = {2015.06.29}
}

@Article{Atilgan2001,
  Title                    = {Anisotropy of fluctuation dynamics of proteins with an elastic network model.},
  Author                   = {Atilgan, A. R. and Durell, S. R. and Jernigan, R. L. and Demirel, M. C. and Keskin, O. and Bahar, I.},
  Journal                  = {Biophys J},
  Year                     = {2001},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {505--515},
  Volume                   = {80},

  Abstract                 = {Fluctuations about the native conformation of proteins have proven to be suitably reproduced with a simple elastic network model, which has shown excellent agreement with a number of different properties for a wide variety of proteins. This scalar model simply investigates the magnitudes of motion of individual residues in the structure. To use the elastic model approach further for developing the details of protein mechanisms, it becomes essential to expand this model to include the added details of the directions of individual residue fluctuations. In this paper a new tool is presented for this purpose and applied to the retinol-binding protein, which indicates enhanced flexibility in the region of entry to the ligand binding site and for the portion of the protein binding to its carrier protein.},
  Doi                      = {10.1016/S0006-3495(01)76033-X},
  Institution              = {School of Engineering and Polymer Research Center, Bogazici University, and TUBITAK Advanced Polymeric Materials Research Center, Bebek 80815, Istanbul, Turkey.},
  Keywords                 = {Anisotropy; Binding Sites; Biophysical Phenomena; Biophysics; Crystallography, X-Ray; Elasticity; Models, Molecular; Protein Binding; Protein Conformation; Proteins, chemistry; Retinol-Binding Proteins, chemistry; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0006-3495(01)76033-X},
  Pmid                     = {11159421},
  Timestamp                = {2014.02.07}
}

@Article{Auffinger:1996,
  Title                    = {H--bond Stability in the t{RNA} Anticodon Hairpin: 3 ns of Multiple Molecular Dynamics Simulations},
  Author                   = {Auffinger, P. and Westhof, E.},
  Journal                  = BPJ,
  Year                     = {1996},
  Number                   = {4},
  Pages                    = {940--954},
  Volume                   = {71},

  File                     = {:pdfs/Auffinger1996.pdf:PDF}
}

@Article{Babin2011,
  Title                    = {The $\alpha$-sheet: A missing-in-action secondary structure?},
  Author                   = {Babin, Volodymyr and Roland, Christopher and Sagui, Celeste},
  Journal                  = {Proteins: Structure, Function, and Bioinformatics},
  Year                     = {2011},
  Number                   = {3},
  Pages                    = {937--946},
  Volume                   = {79},

  Publisher                = {Wiley Online Library}
}

@Article{Babu2011,
  Title                    = {Intrinsically disordered proteins: regulation and disease},
  Author                   = {Babu, M Madan and van der Lee, Robin and de Groot, Natalia Sanchez and Gsponer, J{\"o}rg},
  Journal                  = {Current opinion in structural biology},
  Year                     = {2011},
  Number                   = {3},
  Pages                    = {432--440},
  Volume                   = {21},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.17}
}

@Article{Bahi2013,
  Title                    = {Computational investigations of folded self-avoiding walks related to protein folding},
  Author                   = {Bahi, Jacques M and Guyeux, Christophe and Mazouzi, Kamel and Philippe, Laurent},
  Journal                  = {Computational biology and chemistry},
  Year                     = {2013},
  Pages                    = {246--256},
  Volume                   = {47},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2014.10.09}
}

@Article{Bakan2009,
  Title                    = {The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding},
  Author                   = {Bakan, Ahmet and Bahar, Ivet},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2009},
  Number                   = {34},
  Pages                    = {14349--14354},
  Volume                   = {106},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2013.11.17}
}

@Article{Baker1983,
  Title                    = {Polyoma Virus 'Hexamer' Tubes Consist of Paired Pentamers.},
  Author                   = {Baker, T. S. and Caspar, D. L. D. and Murakami, W. T.},
  Journal                  = {Nature},
  Year                     = {1983},
  Pages                    = {446--448},
  Volume                   = {303},

  File                     = {Baker1983.pdf:pdfs/Baker1983.pdf:PDF}
}

@Article{Baldauf1999,
  Title                    = {A Search for the Origins of Animals and Fungi: Comparing and Combining Molecular Data.},
  Author                   = {Baldauf},
  Journal                  = {Am Nat},
  Year                     = {1999},

  Month                    = {Oct},
  Number                   = {S4},
  Pages                    = {S178--S188},
  Volume                   = {154},

  Abstract                 = {Green plants, animals, and fungi have long held our interest as complex, largely multicellular eukaryotes of indeterminate origin. Considerable progress has now been made toward understanding the evolutionary relationships among these taxa as well as identifying their closest protistan relatives. An exclusive animal-fungal clade (the Opisthokonta) is now widely accepted based on an insertion in the protein synthesis elongation factor 1alpha (EF-1alpha) and molecular phylogenies of ribosomal RNAs and the conservative proteins actin, alpha-tubulin, beta-tubulin, and EF-1alpha. Protein data also suggest that the cellular (dictyostelid) and acellular (myxogastrid) slime molds are a close outgroup to the animal-fungal clade. Subsequent sequencing and phylogenetic analysis of EF-1alpha sequences very strongly support a monophyletic slime mold clade (the Mycetozoa or Eumycetozoa), which also includes the lesser-known protostelid slime molds. Monophyly of the opisthokont and mycetozoan 
clades, exclusive of green plants, is suggested by individual analyses of EF-1alpha and actin and given strong support by concatenated protein data. Neither the monophyly of the slime molds nor their close relationship to animals and fungi are consistently supported by ribosomal RNA data. Thus, it appears unlikely that any single molecule will accurately reconstruct all higher-order taxonomy.},
  Owner                    = {ranjan},
  Pii                      = {AN991007},
  Pmid                     = {10527926},
  Timestamp                = {2009.11.27}
}

@Article{Bapteste2004,
  Title                    = {On the conceptual difficulties in rooting the tree of life.},
  Author                   = {E. Bapteste and C. Brochier},
  Journal                  = {Trends Microbiol},
  Year                     = {2004},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {9--13},
  Volume                   = {12},

  Abstract                 = {Rooting the 'tree of life' represents a major challenge for evolutionists. Without such a root, many of the first steps in biological evolution cannot be reconstructed. However, the nature of the last common ancestor of all living beings remains elusive, proof of the difficulty in shedding light on such an ancient event. Here, we highlight the practical difficulties and conceptual reasons that hinder the placement of a universal root. We discuss how, when addressing the question of the root of the tree of life, scientists unconsciously risk using the reasoning pattern of ancient skeptics, unfortunately known only to lead to further uncertainty. Hence, we argue that the root of the tree of life will not be established unless radically new approaches are considered. We propose a hypothetical means to overcome several of the conceptual difficulties pointed out, and suggest that a so-called 'transition analysis' of the structural evolution of the cytoplasmic membrane might be 
helpful, especially if evolutionary steps involving the rooting issue are polarized accounting more for physicochemical knowledge rather than hypothetical and controversial selective advantages.},
  Institution              = {Equipe Phylog?nie, Bioinformatique et G?nome, UMR CNRS 7622, Universit? Pierre et Marie Curie, 9 quai St. Bernard, 75005 Paris, France. eric.baptiste@snv.jussieu.fr},
  Keywords                 = {Cell Membrane, genetics/physiology; Eukaryotic Cells; Evolution, Molecular; Phylogeny; Prokaryotic Cells},
  Owner                    = {ranjan},
  Pii                      = {S0966842X0300307X},
  Pmid                     = {14700546},
  Timestamp                = {2009.10.01}
}

@Article{Bar-Num1994,
  Title                    = {Assemblies of Free Amino Acids as Possible Prebiotic Catalysts},
  Author                   = {A. Bar-Nun and E. Kochavi and S.Bar.Nun},
  Journal                  = {J Mol Evol.},
  Year                     = {1994},
  Pages                    = {116-122},
  Volume                   = {39},

  Owner                    = {ranjan},
  Timestamp                = {2012.04.08}
}

@Article{Barquet1997,
  Title                    = {Smallpox: the triumph over the most terrible of the ministers of death},
  Author                   = {Barquet, N. and Domingo, P.},
  Journal                  = {Ann Intern Med.},
  Year                     = {1997},
  Number                   = {8 Pt 1},
  Pages                    = {635-642},
  Volume                   = {127},

  File                     = {Barquet1997.pdf:pdfs/Barquet1997.pdf:PDF}
}

@Article{Barraclough2001,
  Title                    = {Evolutionary rates and species diversity in flowering plants.},
  Author                   = {T. G. Barraclough and V. Savolainen},
  Journal                  = {Evolution},
  Year                     = {2001},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {677--683},
  Volume                   = {55},

  Abstract                 = {Genetic change is a necessary component of speciation, but the relationship between rates of speciation and molecular evolution remains unclear. We use recent phylogenetic data to demonstrate a positive relationship between species numbers and the rate of neutral molecular evolution in flowering plants (in both plastid and nuclear genes). Rates of protein and morphological evolution also correlate with the neutral substitution rate, but not with species numbers. Our findings reveal a link between the rate of neutral molecular change within populations and the evolution of species diversity.},
  Institution              = {Department of Biology and NERC Centre for Population Biology, Imperial College at Silwood Park, Ascot, Berkshire, United Kingdom. t.barraclough@ic.ac.uk},
  Keywords                 = {Angiosperms, genetics; DNA, Plant, genetics; DNA, Ribosomal, genetics; Evolution, Molecular; Phylogeny; Plant Proteins, genetics; Regression Analysis; Ribulose-Bisphosphate Carboxylase; Species Specificity},
  Owner                    = {ranjan},
  Pmid                     = {11392385},
  Timestamp                = {2011.04.26}
}

@Article{Barton2000,
  Title                    = {Genetic hitchhiking.},
  Author                   = {N. H. Barton},
  Journal                  = {Philos Trans R Soc Lond B Biol Sci},
  Year                     = {2000},

  Month                    = {Nov},
  Number                   = {1403},
  Pages                    = {1553--1562},
  Volume                   = {355},

  Abstract                 = {Selection on one or more genes inevitably perturbs other genes, even when those genes have no direct effect on fitness. This article reviews the theory of such genetic hitchhiking, concentrating on effects on neutral loci. Maynard Smith and Haigh introduced the classical case where the perturbation is due to a single favourable mutation. This is contrasted with the apparently distinct effects of inherited variation in fitness due to loosely linked loci. A model of fluctuating selection is analysed which bridges these alternative treatments. When alleles sweep between extreme frequencies at a rate lambda, the rate of drift is increased by a factor (1 + E[1/pq]lambda/(2(2lambda + r))), where the recombination rate r is much smaller than the strength of selection. In spatially structured populations, the effects of any one substitution are weaker, and only cause a local increase in the frequency of a neutral allele. This increase depends primarily on the rate of recombination 
relative to selection (r/s), and more weakly, on the neighbourhood size, Nb = 4(pi rho sigma)2. Spatial subdivision may allow local selective sweeps to occur more frequently than is indicated by the overall rate of molecular evolution. However, it seems unlikely that such sweeps can be sufficiently frequent to increase significantly the drift of neutral alleles.},
  Institution              = {Institute of Cell, Animal and Population Biology, University of Edinburgh, UK. n.barton@ed.ac.uk},
  Keywords                 = {Animals; Genes; Selection, Genetic},
  Owner                    = {ranjan},
  Pmid                     = {11127900},
  Timestamp                = {2011.05.02}
}

@Article{Baruah2015,
  Title                    = {Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads},
  Author                   = {Baruah, Anupaul and Rani, Pooja and Biswas, Parbati},
  Journal                  = {Scientific reports},
  Year                     = {2015},
  Volume                   = {5},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2015.09.17}
}

@Article{Basak2005,
  Title                    = {Correlations between genomic GC levels and optimal growth temperatures: some comments.},
  Author                   = {Basak, Surajit and Mandal, Syamsundar and Ghosh, Tapash Chandra},
  Journal                  = {Biochem Biophys Res Commun},
  Year                     = {2005},

  Month                    = {Feb},
  Number                   = {4},
  Pages                    = {969--970},
  Volume                   = {327},

  Abstract                 = {Regarding the existence of any specific correlation between optimal growth temperature and genomic GC levels, Musto et al. [FEBS Lett. 573 (2004) 73] have recently performed analysis on 20 prokaryotic families and showed that in most of the families there exists a positive correlation between these two parameters. On the basis of these results they claimed that optimal growth temperature is one of the factors that influence genomic GC composition in prokaryotes. In a subsequent article, Marashi and Ghalanbor [Biochem. Biophys. Res. Commun. 325 (2004) 381] have demonstrated that the correlation values change substantially when very few points in some of the families were excluded from the data set of Musto et al. [FEBS Lett. 573 (2004) 73]. But Marashi and Ghalanbor have not provided any reason behind this. The points excluded by Marashi and Ghalanbor are actually the outliers in the data set, which strongly affect the correlation coefficients. But the presence of outliers in 
large data set hardly had any effect on the correlation values. Marashi and Ghalanbor have excluded points from only those families that have small sample sizes and observed a substantial change in correlation coefficient values. Therefore, we argue that any conclusion drawn for a small sample size having outliers is always questionable. Although Musto's approach is a novel one, but to make any generalization one needs to be careful about the flawlessness in the data set.},
  Institution              = {Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India.},
  Keywords                 = {Base Composition; Cell Proliferation; Genome; Prokaryotic Cells, cytology; Temperature},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0006-291X(04)02912-2},
  Pmid                     = {15652489},
  Timestamp                = {2012.09.26}
}

@Article{Basiuk2001,
  Title                    = {Catalysis of peptide formation by inorganic oxides: high efficiency of alumina under mild conditions on the Earth-like planets.},
  Author                   = {V. A. Basiuk and J. Sainz-Rojas},
  Journal                  = {Adv Space Res},
  Year                     = {2001},
  Number                   = {2},
  Pages                    = {225--230},
  Volume                   = {27},

  Abstract                 = {Amino acid condensation catalyzed by inorganic oxides is a widely recognized way for prebiotic peptide formation. Silica and alumina are widely distributed in the Earth-like planets' crust as minerals of different complexity, and thus are attractive model catalysts for the studies of abiotic peptide synthesis. Experiments performed in other laboratories have shown that this process can be efficient at > 80 degrees C, which is not easy to find on the planetary surface in combination with sufficient concentrations of amino acids and necessary catalysts. In the present work we tested catalytic activity of three forms of alumina (which proved to be an efficient catalyst for this process) in the intermolecular condensation of L-alanine. We expanded the temperature interval down to 55 degrees C and used the simplest permanent heating procedure, without employing fluctuating drying/wetting conditions. The most important finding is that even under the lowest temperature considered (i.e. 
55 degrees C), short peptide formation can be detected already after 10-30 days of heating. This fact implies that the abiotic peptide formation might occur in a wide variety of planetary environments, without need for high temperatures, given the presence of amino acid building blocks and alumina-containing minerals.},
  Institution              = {Instituto de Ciencias Nucleares, Universidad Nacional Autonoma de Mexico, Circuito Exterior C.U., A. Postal 70-543, 04510 Mexico D.F., Mexico. basiuk@nuclecu.unam.mx},
  Keywords                 = {Alanine, chemistry; Aluminum Oxide, chemistry; Catalysis; Dimerization; Evolution, Chemical; Hot Temperature; Hydrogen-Ion Concentration; Peptides, chemical synthesis; Temperature},
  Owner                    = {ranjan},
  Pmid                     = {11605636},
  Timestamp                = {2009.11.29}
}

@Article{Bastolla2004,
  Title                    = {Genomic determinants of protein folding thermodynamics in prokaryotic organisms.},
  Author                   = {Bastolla, Ugo and Moya, Andr\'{e}s and Viguera, Enrique and {van Ham}, Roeland C H J.},
  Journal                  = {J Mol Biol},
  Year                     = {2004},

  Month                    = {Nov},
  Number                   = {5},
  Pages                    = {1451--1466},
  Volume                   = {343},

  Abstract                 = {Here we investigate how thermodynamic properties of orthologous proteins are influenced by the genomic environment in which they evolve. We performed a comparative computational study of 21 protein families in 73 prokaryotic species and obtained the following main results. (i) Protein stability with respect to the unfolded state and with respect to misfolding are anticorrelated. There appears to be a trade-off between these two properties, which cannot be optimized simultaneously. (ii) Folding thermodynamic parameters are strongly correlated with two genomic features, genome size and G+C composition. In particular, the normalized energy gap, an indicator of folding efficiency in statistical mechanical models of protein folding, is smaller in proteins of organisms with a small genome size and a compositional bias towards A+T. Such genomic features are characteristic for bacteria with an intracellular lifestyle. We interpret these correlations in light of mutation pressure and 
natural selection. A mutational bias toward A+T at the DNA level translates into a mutational bias toward more hydrophobic (and in general more interactive) proteins, a consequence of the structure of the genetic code. Increased hydrophobicity renders proteins more stable against unfolding but less stable against misfolding. Proteins with high hydrophobicity and low stability against misfolding occur in organisms with reduced genomes, like obligate intracellular bacteria. We argue that they are fixed because these organisms experience weaker purifying selection due to their small effective population sizes. This interpretation is supported by the observation of a high expression level of chaperones in these bacteria. Our results indicate that the mutational spectrum of a genome and the strength of selection significantly influence protein folding thermodynamics.},
  Keywords                 = {Archaea, genetics/metabolism; Archaeal Proteins, genetics/metabolism; Bacteria, genetics/metabolism; Bacterial Proteins, genetics/metabolism; Computational Biology; Genome, Archaeal; Genome, Bacterial; Hydrophobic and Hydrophilic Interactions; Models, Molecular; Principal Component Analysis; Protein Denaturation; Protein Folding; Sequence Homology, Amino Acid; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(04)01086-1},
  Pmid                     = {15491623},
  Timestamp                = {2012.09.30}
}

@Article{Basu2008,
  Title                    = {Evolution of protein domain promiscuity in eukaryotes.},
  Author                   = {Basu, Malay Kumar and Carmel, Liran and Rogozin, Igor B. and Koonin, Eugene V.},
  Journal                  = {Genome Res},
  Year                     = {2008},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {449--461},
  Volume                   = {18},

  Abstract                 = {Numerous eukaryotic proteins contain multiple domains. Certain domains show a tendency to occur in diverse domain architectures and can be considered "promiscuous." These promiscuous domains are, typically, involved in protein-protein interactions and play crucial roles in interaction networks, particularly those that contribute to signal transduction. A systematic comparative-genomic analysis of promiscuous domains in eukaryotes is described. Two quantitative measures of domain promiscuity are introduced and applied to the analysis of 28 genomes of diverse eukaryotes. Altogether, 215 domains are identified as strongly promiscuous. The fraction of promiscuous domains in animals is shown to be significantly greater than that in fungi or plants. Evolutionary reconstructions indicate that domain promiscuity is a volatile, relatively fast-changing feature of eukaryotic proteins, with few domains remaining promiscuous throughout the evolution of eukaryotes. Some domains appear to 
have attained promiscuity independently in different lineages, for example, animals and plants. It is proposed that promiscuous domains persist within a relatively small pool of evolutionarily stable domain combinations from which numerous rare architectures emerge during evolution. Domain promiscuity positively correlates with the number of experimentally detected domain interactions and with the strength of purifying selection affecting a domain. Thus, evolution of promiscuous domains seems to be constrained by the diversity of their interaction partners. The set of promiscuous domains is enriched for domains mediating protein-protein interactions that are involved in various forms of signal transduction, especially in the ubiquitin system and in chromatin. Thus, a limited repertoire of promiscuous domains makes a major contribution to the diversity and evolvability of eukaryotic proteomes and signaling networks.},
  Doi                      = {10.1101/gr.6943508},
  Institution              = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.},
  Keywords                 = {Animals; Evolution, Molecular; Fungal Proteins, chemistry; Genomics; Phylogeny; Plant Proteins, chemistry; Protein Interaction Domains and Motifs; Protein Structure, Tertiary},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {gr.6943508},
  Pmid                     = {18230802},
  Timestamp                = {2014.02.11}
}

@Article{Becke1993,
  Title                    = {Density-functional thermochemistry. III. The role of exact exchange},
  Author                   = {Becke, Axel D},
  Journal                  = {The Journal of Chemical Physics},
  Year                     = {1993},
  Number                   = {7},
  Pages                    = {5648--5652},
  Volume                   = {98},

  Owner                    = {ranjan},
  Publisher                = {AIP Publishing},
  Timestamp                = {2014.07.23}
}

@Book{Behr2008,
  Title                    = {The Lock-and-Key Principle, The State of the Art--100 Years On},
  Author                   = {Behr, Jean-Paul},
  Publisher                = {John Wiley \& Sons},
  Year                     = {2008},
  Volume                   = {1},

  Owner                    = {ranjan},
  Timestamp                = {2013.07.20}
}

@Article{Beke2006,
  Title                    = {Toward a rational design of beta-peptide structures.},
  Author                   = {Beke, Tam{\'{a}}s and Somlai, Csaba and Perczel, Andr{\'{a}}s},
  Journal                  = {J Comput Chem},
  Year                     = {2006},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {20--38},
  Volume                   = {27},

  Abstract                 = {Intrinsic conformational characteristics of beta-peptides built up from simple achiral and chiral beta-amino acid residues (i.e., HCO-beta-Ala-NH2, HCO-beta-Abu-NH2) were studied using quantum chemical calculations and 1H-NMR spectroscopy. A conformer-based systematic and uniform nomenclature was introduced to differentiate conformers. Geometry optimizations were performed on all homoconformers of both HCO-(beta-Ala)(k)-NH2 and HCO-(beta-Abu)(k)-NH2 (1 < or = k < or = 6) model systems at the RHF/3-21G and RHF/6-311++G(d, p) levels of theory. To test for accuracy and precision, additional computations were carried out at several levels of theory [e.g., RHF/6-31G(d), and B3LYP/6-311++G(d, p)]. To display the folding preference, the relative stability of selected conformers as function of the length of the polypeptide chain was determined. Ab initio population distribution of hexapeptides and the conformational ensemble of synthetic models composed of beta-Ala and beta-Abu studied 
using 1H-NMR in different solvents were compared at a range of temperatures. Helical preference induced by various steric effects of nonpolar side chains was tested using higher level ab initio methods for well-known model systems such as: HCO-(beta-HVal-beta-HAla-beta-HLeu)2-NH2, HCO-(ACHC)6-NH2, HCO-(trans-ACPC)6-NH2, and HCO-(cis-ACPC)6-NH2. The relative stabilities determined by theoretical methods agreed well with most experimental data, supporting the theory that the local conformational preference influenced by steric effects is a key determining factor of the global fold both in solution and in the gas phase.},
  Doi                      = {10.1002/jcc.20299},
  Institution              = {Department of Organic Chemistry, Eötvös L. Univ., P.O. Box 32, H-1518 Budapest 112, Hungary.},
  Keywords                 = {Magnetic Resonance Spectroscopy; Models, Molecular; Oligopeptides, chemistry; Protein Structure, Secondary; Solvents},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {16247761},
  Timestamp                = {2014.04.26}
}

@Article{Bella1994,
  Title                    = {Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution},
  Author                   = {Bella, Jordi and Eaton, Mark and Brodsky, Barbara and Berman, Helen M},
  Journal                  = {Science},
  Year                     = {1994},
  Number                   = {5182},
  Pages                    = {75--81},
  Volume                   = {266},

  Publisher                = {American Association for the Advancement of Science}
}

@Article{Belozersky1958,
  Title                    = {A correlation between the compositions of deoxyribonucleic and ribonucleic acids.},
  Author                   = {Belozersky, A. N. And Spirin, A. S.},
  Journal                  = {Nature},
  Year                     = {1958},

  Month                    = {Jul},
  Number                   = {4628},
  Pages                    = {111--112},
  Volume                   = {182},

  Keywords                 = {DNA; RNA},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {13566202},
  Timestamp                = {2012.09.26}
}

@Article{Ben-Naim2012,
  Title                    = {Shannon's Measure of Information and the Thermodynamic Entropy},
  Author                   = {Arieh Ben-Naim},
  Journal                  = {AIP Conference Proceedings},
  Year                     = {2012},
  Pages                    = {129--142},
  Volume                   = {1443},

  Owner                    = {ranjan},
  Timestamp                = {2016.09.04}
}

@Article{Benner1993,
  Title                    = {Empirical and structural models for insertions and deletions in the divergent evolution of proteins.},
  Author                   = {S. A. Benner and M. A. Cohen and G. H. Gonnet},
  Journal                  = {J Mol Biol},
  Year                     = {1993},

  Month                    = {Feb},
  Number                   = {4},
  Pages                    = {1065--1082},
  Volume                   = {229},

  Abstract                 = {The exhaustive matching of the protein sequence database makes possible a broadly based study of insertions and deletions (indels) during divergent evolution. In this study, the probability of a gap in an alignment of a pair of homologous protein sequences was found to increase with the evolutionary distance measured in PAM units (number of accepted point mutations per 100 amino acid residues). A relationship between the average number of amino acid residues between indels and evolutionary distance suggests that a unit 30 to 40 amino acid residues in length remains, on average, undisrupted by indels during divergent evolution. Further, the probability of a gap was found to be inversely proportional to gap length raised to the 1.7 power. This empirical law fits closely over the entire range of gap lengths examined. Gap length distribution is largely independent of evolutionary distance. These results rule out the widely used linear gap penalty as a satisfactory formula for 
scoring gaps when constructing alignments. Further, the observed gap length distribution can be explained by a simple model of selective pressures governing the acceptance of indels during divergent evolution. Finally, this model provides theoretical support for using indels as part of ``parsing algorithms'', important in the de novo prediction of the folded structure of proteins from the sequence data.},
  Institution              = {Institute for Organic Chemistry, Swiss Federal Institute of Technology, Zurich.},
  Keywords                 = {Amino Acid Sequence; Amino Acids, chemistry; Databases, Factual; Evolution; Genetic Variation; Models, Chemical; Models, Genetic; Molecular Sequence Data; Probability; Proteins, chemistry/genetics; Sequence Deletion; Sequence Homology, Amino Acid},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(83)71105-8},
  Pmid                     = {8445636},
  Timestamp                = {2010.05.19}
}

@Article{Bennett1984,
  Title                    = {Structural and Functional Aspects of Domain Motions in Protein},
  Author                   = {Bennett, William S and Huber, Robert and Engel, J{\"U}Rgen},
  Journal                  = {Critical Reviews in Biochemistry and Molecular Biology},
  Year                     = {1984},
  Number                   = {4},
  Pages                    = {291--384},
  Volume                   = {15},

  Owner                    = {ranjan},
  Publisher                = {Informa UK Ltd UK},
  Timestamp                = {2013.08.15}
}

@Article{Bentley2004,
  Title                    = {Comparative genomic structure of prokaryotes.},
  Author                   = {Bentley, Stephen D. and Parkhill, Julian},
  Journal                  = {Annu Rev Genet},
  Year                     = {2004},
  Pages                    = {771--792},
  Volume                   = {38},

  Abstract                 = {Recent advances in DNA-sequencing technologies have made available an enormous resource of data for the study of bacterial genomes. The broad sample of complete genomes currently available allows us to look at variation in the gross features and characteristics of genomes while the detail of the sequences reveal some of the mechanisms by which these genomes evolve. This review aims to describe bacterial genome structures according to current knowledge and proposed hypotheses. We also describe examples where mechanisms of genome evolution have acted in the adaptation of bacterial species to particular niches.},
  Institution              = {Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. sdb@sanger.ac.uk},
  Keywords                 = {Bacteria, genetics; Base Composition; Databases, Genetic; Evolution, Molecular; Gene Order; Genes, Bacterial; Genome Components; Genome, Bacterial; Species Specificity; Synteny},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {15568993},
  Timestamp                = {2012.09.27}
}

@Article{Bentley2004a,
  Title                    = {Comparative genomic structure of prokaryotes.},
  Author                   = {Stephen D Bentley and Julian Parkhill},
  Journal                  = {Annu Rev Genet},
  Year                     = {2004},
  Pages                    = {771--792},
  Volume                   = {38},

  Abstract                 = {Recent advances in DNA-sequencing technologies have made available an enormous resource of data for the study of bacterial genomes. The broad sample of complete genomes currently available allows us to look at variation in the gross features and characteristics of genomes while the detail of the sequences reveal some of the mechanisms by which these genomes evolve. This review aims to describe bacterial genome structures according to current knowledge and proposed hypotheses. We also describe examples where mechanisms of genome evolution have acted in the adaptation of bacterial species to particular niches.},
  Institution              = {Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. sdb@sanger.ac.uk},
  Keywords                 = {Bacteria, genetics; Base Composition; Databases, Genetic; Evolution, Molecular; Gene Order; Genes, Bacterial; Genome Components; Genome, Bacterial; Species Specificity; Synteny},
  Owner                    = {ranjan},
  Pmid                     = {15568993},
  Timestamp                = {2010.09.27}
}

@Article{Berezovsky2005,
  Title                    = {Entropic stabilization of proteins and its proteomic consequences.},
  Author                   = {Igor N Berezovsky and William W Chen and Paul J Choi and Eugene I Shakhnovich},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2005},

  Month                    = {Sep},
  Number                   = {4},
  Pages                    = {e47},
  Volume                   = {1},

  Abstract                 = {Evolutionary traces of thermophilic adaptation are manifest, on the whole-genome level, in compositional biases toward certain types of amino acids. However, it is sometimes difficult to discern their causes without a clear understanding of underlying physical mechanisms of thermal stabilization of proteins. For example, it is well-known that hyperthermophiles feature a greater proportion of charged residues, but, surprisingly, the excess of positively charged residues is almost entirely due to lysines but not arginines in the majority of hyperthermophilic genomes. All-atom simulations show that lysines have a much greater number of accessible rotamers than arginines of similar degree of burial in folded states of proteins. This finding suggests that lysines would preferentially entropically stabilize the native state. Indeed, we show in computational experiments that arginine-to-lysine amino acid substitutions result in noticeable stabilization of proteins. We then hypothesize 
that if evolution uses this physical mechanism as a complement to electrostatic stabilization in its strategies of thermophilic adaptation, then hyperthermostable organisms would have much greater content of lysines in their proteomes than comparably sized and similarly charged arginines. Consistent with that, high-throughput comparative analysis of complete proteomes shows extremely strong bias toward arginine-to-lysine replacement in hyperthermophilic organisms and overall much greater content of lysines than arginines in hyperthermophiles. This finding cannot be explained by genomic GC compositional biases or by the universal trend of amino acid gain and loss in protein evolution. We discovered here a novel entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state and demonstrated its immediate proteomic implications. Our study provides an example of how analysis of a fundamental physical mechanism of thermostability helps to resolve a puzzle in 
comparative genomics as to why amino acid compositions of hyperthermophilic proteomes are significantly biased toward lysines but not similarly charged arginines.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America.},
  Keywords                 = {Aminopeptidases, metabolism; Arginine, metabolism; Computational Biology; Computer Simulation; Cytochromes c, metabolism; Endopeptidases, metabolism; Entropy; Enzyme Stability; Escherichia coli, enzymology; Genome, genetics; Lysine, metabolism; Monte Carlo Method; Mutation, genetics; Protein Folding; Proteome, chemistry/metabolism; Proteomics; Temperature; Thermus thermophilus, enzymology},
  Owner                    = {ranjan},
  Pmid                     = {16201009},
  Timestamp                = {2009.12.05}
}

@Article{Berezovsky2005a,
  Title                    = {Physics and evolution of thermophilic adaptation.},
  Author                   = {Igor N Berezovsky and Eugene I Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2005},

  Month                    = {Sep},
  Number                   = {36},
  Pages                    = {12742--12747},
  Volume                   = {102},

  Abstract                 = {Analysis of structures and sequences of several hyperthermostable proteins from various sources reveals two major physical mechanisms of their thermostabilization. The first mechanism is "structure-based," whereby some hyperthermostable proteins are significantly more compact than their mesophilic homologues, while no particular interaction type appears to cause stabilization; rather, a sheer number of interactions is responsible for thermostability. Other hyperthermostable proteins employ an alternative, "sequence-based" mechanism of their thermal stabilization. They do not show pronounced structural differences from mesophilic homologues. Rather, a small number of apparently strong interactions is responsible for high thermal stability of these proteins. High-throughput comparative analysis of structures and complete genomes of several hyperthermophilic archaea and bacteria revealed that organisms develop diverse strategies of thermophilic adaptation by using, to a varying 
degree, two fundamental physical mechanisms of thermostability. The choice of a particular strategy depends on the evolutionary history of an organism. Proteins from organisms that originated in an extreme environment, such as hyperthermophilic archaea (Pyrococcus furiosus), are significantly more compact and more hydrophobic than their mesophilic counterparts. Alternatively, organisms that evolved as mesophiles but later recolonized a hot environment (Thermotoga maritima) relied in their evolutionary strategy of thermophilic adaptation on "sequence-based" mechanism of thermostability. We propose an evolutionary explanation of these differences based on physical concepts of protein designability.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.},
  Keywords                 = {Acclimatization, physiology; Amino Acids, chemistry; Archaeal Proteins, chemistry/genetics/metabolism; Bacterial Proteins, chemistry/genetics/metabolism; Biophysical Phenomena; Biophysics; Evolution; Protein Denaturation; Protein Folding; Temperature; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {0503890102},
  Pmid                     = {16120678},
  Timestamp                = {2009.12.05}
}

@Book{Berg2006,
  Title                    = {Biochemistry, International Edition},
  Author                   = {Berg, Jeremy M and Tymoczko, John L and Stryer, Lubert},
  Publisher                = {WH Freeman \& Co.},
  Year                     = {2010},

  Address                  = {New York},
  Edition                  = {7}
}

@Article{Berman2000,
  Title                    = {The protein data bank},
  Author                   = {Berman, Helen M and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, TN and Weissig, Helge and Shindyalov, Ilya N and Bourne, Philip E},
  Journal                  = {Nucleic acids research},
  Year                     = {2000},
  Number                   = {1},
  Pages                    = {235--242},
  Volume                   = {28},

  Owner                    = {ranjan},
  Publisher                = {Oxford Univ Press},
  Timestamp                = {2013.11.19}
}

@Article{Bernardi1985a,
  Title                    = {Codon usage and genome composition.},
  Author                   = {Bernardi, G. and Bernardi, G.},
  Journal                  = {J Mol Evol},
  Year                     = {1985},
  Number                   = {4},
  Pages                    = {363--365},
  Volume                   = {22},

  Abstract                 = {The GC levels of codon third positions from 49 genomes covering a wide phylogenetic range are linearly correlated with the GC levels of the corresponding genomes. Three different relationships have been found: one for prokaryotes and viruses, one for lower eukaryotes, and one for vertebrates. All points not fitting the first relationship can be brought into quasi coincidence with it when plotted against GC levels of coding sequences.},
  Keywords                 = {Animals; Bacteria, genetics; Base Sequence; Codon; Genes; Phylogeny; RNA, Messenger; Species Specificity; Viruses, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {3936938},
  Timestamp                = {2012.09.26}
}

@Article{Bershtein2008,
  Title                    = {Intense neutral drifts yield robust and evolvable consensus proteins},
  Author                   = {Bershtein, Shimon and Goldin, Korina and Tawfik, Dan S},
  Journal                  = {Journal of molecular biology},
  Year                     = {2008},
  Number                   = {5},
  Pages                    = {1029--1044},
  Volume                   = {379},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.30}
}

@Article{Bertin2005,
  Title                    = {Real-space analysis of inherent structures},
  Author                   = {Bertin, Eric},
  Journal                  = {EPL (Europhysics Letters)},
  Year                     = {2005},
  Number                   = {3},
  Pages                    = {452},
  Volume                   = {71},

  Owner                    = {ranjan},
  Publisher                = {IOP Publishing},
  Timestamp                = {2015.09.22}
}

@Article{Betancourt2009,
  Title                    = {Another look at the conditions for the extraction of protein knowledge-based potentials.},
  Author                   = {Marcos R Betancourt},
  Journal                  = {Proteins},
  Year                     = {2009},

  Month                    = {Jul},
  Number                   = {1},
  Pages                    = {72--85},
  Volume                   = {76},

  Abstract                 = {Protein knowledge-based potentials are effective free energies obtained from databases of known protein structures. They are used to parameterize coarse-grained protein models in many folding simulation and structure prediction methods. Two common approaches are used in the derivation of knowledge-based potentials. One assumes that the energy parameters optimize the native structure stability. The other assumes that interaction events are related to their energies according to the Boltzmann distribution, and that they are distributed independently of other events, that is, the quasi-chemical approximation. Here, these assumptions are systematically tested by extracting contact energies from artificial databases of lattice proteins with predefined pairwise contact energies. Databases of protein sequences are designed to either satisfy the Boltzmann distribution at high or low temperatures, or to simultaneously optimize the native stability and folding kinetics. It is found that 
the quasi-chemical approximation, with the ideal reference state, accurately reproduce the true energies for high temperature Boltzmann distributed sequences (weakly interacting residues), but less accurately at low temperatures, where the sequences correspond to energy minima and the residues are strongly interacting. To overcome this problem, an iterative procedure for Boltzmann distributed sequences is introduced, which accounts for interacting residue correlations and eliminates the need for the quasi-chemical approximation. In this case, the energies are accurately reproduced at any ensemble temperature. However, when the database of sequences designed for optimal stability and kinetics is used, the energy correlation is less than optimal using either method, exhibiting random and systematic deviations from linearity. Therefore, the assumption that native structures are maximally stable or that sequences are determined according to the Boltzmann distribution seems to be inadequate for obtaining accurate 
energies. The limited number of sequences in the database and the inhomogeneous concentration of amino acids from one structure to another do not seem to be major obstacles for improving the quality of the extracted pairwise energies, with the exception of repulsive interactions.},
  Institution              = {Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA. mbetancourt@mailaps.org},
  Keywords                 = {Amino Acid Sequence; Computational Biology, methods; Computer Simulation; Models, Molecular; Protein Conformation; Protein Folding; Proteins, chemistry; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {19089977},
  Timestamp                = {2011.10.24}
}

@Article{Bhattacharyya2006,
  Title                    = {The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway.},
  Author                   = {Bhattacharyya, Roby P. and Reményi, Attila and Good, Matthew C. and Bashor, Caleb J. and Falick, Arnold M. and Lim, Wendell A.},
  Journal                  = {Science},
  Year                     = {2006},

  Month                    = {Feb},
  Number                   = {5762},
  Pages                    = {822--826},
  Volume                   = {311},

  Abstract                 = {Scaffold proteins organize signaling proteins into pathways and are often viewed as passive assembly platforms. We found that the Ste5 scaffold has a more active role in the yeast mating pathway: A fragment of Ste5 allosterically activated autophosphorylation of the mitogen-activated protein kinase Fus3. The resulting form of Fus3 is partially active-it is phosphorylated on only one of two key residues in the activation loop. Unexpectedly, at a systems level, autoactivated Fus3 appears to have a negative regulatory role, promoting Ste5 phosphorylation and a decrease in pathway transcriptional output. Thus, scaffolds not only direct basic pathway connectivity but can precisely tune quantitative pathway input-output properties.},
  Doi                      = {10.1126/science.1120941},
  Institution              = {Department of Cellular and Molecular Pharmacology, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA.},
  Keywords                 = {Adaptor Proteins, Signal Transducing, chemistry/genetics/metabolism; Allosteric Regulation; Amino Acid Motifs; Binding Sites; Crystallography, X-Ray; Down-Regulation; Enzyme Activation; MAP Kinase Signaling System; Mitogen-Activated Protein Kinases, chemistry/metabolism; Models, Biological; Models, Molecular; Mutation; Pheromones, physiology; Phosphorylation; Protein Binding; Protein Conformation; Protein Structure, Secondary; Protein Structure, Tertiary; Saccharomyces cerevisiae Proteins, chemistry/genetics/metabolism; Saccharomyces cerevisiae, genetics/metabolism; Transcription, Genetic},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {1120941},
  Pmid                     = {16424299},
  Timestamp                = {2013.12.14}
}

@Article{Bienkiewicz2002,
  Title                    = {Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1).},
  Author                   = {Bienkiewicz, Ewa A. and Adkins, Joshua N. and Lumb, Kevin J.},
  Journal                  = {Biochemistry},
  Year                     = {2002},

  Month                    = {Jan},
  Number                   = {3},
  Pages                    = {752--759},
  Volume                   = {41},

  Abstract                 = {p27(Kip1) contributes to cell-cycle regulation by inhibiting cyclin-dependent kinase (Cdk) activity. The p27 Cdk-inhibition domain has an ordered conformation comprising an alpha-helix, a 3(10) helix, and beta-structure when bound to cyclin A-Cdk2. In contrast, the unbound p27 Cdk-inhibition domain is intrinsically disordered (natively unfolded) as shown by circular dichroism spectroscopy, lack of chemical-shift dispersion, and negative heteronuclear nuclear Overhauser effects. The intrinsic disorder is not due to the excision of the Cdk-inhibition domain from p27, since circular dichroism spectra of the full-length protein are also indicative of a largely unfolded protein. Both the inhibition domain and full-length p27 are active as cyclin A-Cdk2 inhibitors. Using circular dichroism and proline mutagenesis, we demonstrate that the unbound p27 Cdk-inhibition domain is not completely unfolded. The domain contains marginally stable helical structure that presages the alpha-helix, 
but not the 3(10) helix, adopted upon binding cyclin A-Cdk2. Increasing or reducing the stability of the partially preformed alpha-helix in the isolated p27 domain with alanine or proline substitutions did not affect formation of the p27-inhibited cyclin A-Cdk2 complex in energetic terms. However, stabilization of the helix with alanine hindered kinetically the formation of the inhibited complex, suggesting that p27 derives a kinetic advantage from intrinsic structural disorder.},
  Institution              = {Department of Biochemistry and Molecular Biology, Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1870, USA.},
  Keywords                 = {Amino Acid Substitution; Binding Sites; Cell Cycle Proteins, chemistry/metabolism; Circular Dichroism; Cyclin-Dependent Kinase Inhibitor p27; Cyclin-Dependent Kinases, antagonists /&/ inhibitors; Humans; Kinetics; Models, Molecular; Mutagenesis, Site-Directed; Phosphorylation; Protein Structure, Secondary; Recombinant Proteins, chemistry/metabolism; Spectrophotometry, Ultraviolet; Thermodynamics; Tumor Suppressor Proteins, chemistry/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {bi015763t},
  Pmid                     = {11790096},
  Timestamp                = {2013.12.11}
}

@Article{Blanchard2000,
  Title                    = {Organellar genes: why do they end up in the nucleus?},
  Author                   = {Blanchard, J. L. and Lynch, M.},
  Journal                  = {Trends Genet},
  Year                     = {2000},

  Month                    = {Jul},
  Number                   = {7},
  Pages                    = {315--320},
  Volume                   = {16},

  Abstract                 = {Many mitochondrial and plastid proteins are derived from their bacterial endosymbiotic ancestors, but their genes now reside on nuclear chromosomes instead of remaining within the organelle. To become an active nuclear gene and return to the organelle as a functional protein, an organellar gene must first be assimilated into the nuclear genome. The gene must then be transcribed and acquire a transit sequence for targeting the protein back to the organelle. On reaching the organelle, the protein must be properly folded and modified, and in many cases assembled in an orderly manner into a larger protein complex. Finally, the nuclear copy must be properly regulated to achieve a fitness level comparable with the organellar gene. Given the complexity in establishing a nuclear copy, why do organellar genes end up in the nucleus? Recent data suggest that these genes are worse off than their nuclear and free-living counterparts because of a reduction in the efficiency of natural 
selection, but do these population-genetic processes drive the movement of genes to the nucleus? We are now at a stage where we can begin to discriminate between competing hypotheses using a combination of experimental, natural population, bioinformatic and theoretical approaches.},
  Institution              = {National Center for Genome Resources, Santa Fe, NM 87505, USA. jlb@ncgr.org},
  Keywords                 = {Cell Nucleus, genetics; Gene Transfer Techniques; Organelles, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0168-9525(00)02053-9},
  Pmid                     = {10858662},
  Timestamp                = {2012.09.10}
}

@Article{Blanchette2008,
  Title                    = {Computational reconstruction of ancestral DNA sequences.},
  Author                   = {Mathauieu Blanchette and Abdoulaye Banir? Diallo and Eric D Green and Webb Miller and David Haussler},
  Journal                  = {Methods Mol Biol},
  Year                     = {2008},
  Pages                    = {171--184},
  Volume                   = {422},

  Abstract                 = {This chapter introduces the problem of ancestral sequence reconstruction: given a set of extant orthologous DNA genomic sequences (or even whole-genomes), together with a phylogenetic tree relating these sequences, predict the DNA sequence of all ancestral species in the tree. Blanchette et al. (1) have shown that for certain sets of species (in particular, for eutherian mammals), very accurate reconstruction can be obtained. We explain the main steps involved in this process, including multiple sequence alignment, insertion and deletion inference, substitution inference, and gene arrangement inference. We also describe a simulation-based procedure to assess the accuracy of the reconstructed sequences. The whole reconstruction process is illustrated using a set of mammalian sequences from the CFTR region.},
  Institution              = {McGill Centre for Bioinformatics, McGill University, Montreal, Canada.},
  Keywords                 = {Animals; Base Sequence; Computational Biology, methods; Computer Simulation; Humans; Molecular Sequence Data; Phylogeny},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {18629667},
  Timestamp                = {2011.09.15}
}

@Article{Blanck1989,
  Title                    = {Primary structure of sensory rhodopsin I, a prokaryotic photoreceptor.},
  Author                   = {A. Blanck and D. Oesterhelt and E. Ferrando and E. S. Schegk and F. Lottspeich},
  Journal                  = {EMBO J},
  Year                     = {1989},

  Month                    = {Dec},
  Number                   = {13},
  Pages                    = {3963--3971},
  Volume                   = {8},

  Abstract                 = {The gene coding for sensory rhodopsin I (SR-I) has been identified in a restriction fragment of genomic DNA from the Halobacterium halobium strain L33. Of the 1014 nucleotides whose sequence was determined, 720 belong to the structural gene of SR-I. In the 5' non-coding region two putative promoter elements and a ribosomal binding site have been identified. The 3' flanking region bears a potential terminator structure. The SR-I protein moiety carries no signal peptide and is not processed at its N terminus. The C terminus, however, lacks the last aspartic acid residue encoded by the gene. Analysis of the primary structure of SR-I reveals no consistent homology with the eukaryotic photoreceptor rhodopsin, but 14\% homology with the halobacterial ion pumps, bacteriorhodopsin (BR) and halorhodopsin (HR). Residues conserved in all three proteins are discussed with respect to their contribution to secondary structure, retinal binding and ion translocation. The aspartic acid residue 
which mediates in BR the reprotonation of the Schiff base (D96) is replaced in SR-I by a tyrosine (Y87). This amino acid replacement is proposed to be of crucial importance in the evolution of the slow-cycling photosensing pigment SR-I.},
  Institution              = {Max-Planck-Institut f?r Biochemie, Martinsried, FRG.},
  Keywords                 = {Amino Acid Sequence; Bacteriorhodopsins, genetics; Base Sequence; DNA, Bacterial, genetics/isolation /&/ purification; Genes, Bacterial; Halobacterium, genetics; Halorhodopsins; Molecular Sequence Data; Peptide Fragments, isolation /&/ purification; Protein Conformation; Sensory Rhodopsins; Sequence Homology, Nucleic Acid; Terminator Regions, Genetic},
  Owner                    = {ranjan},
  Pmid                     = {2591367},
  Timestamp                = {2010.05.09}
}

@Article{Bloom2009,
  Title                    = {In the light of directed evolution: pathways of adaptive protein evolution},
  Author                   = {Bloom, Jesse D and Arnold, Frances H},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2009},
  Number                   = {Supplement 1},
  Pages                    = {9995--10000},
  Volume                   = {106},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2013.11.30}
}

@Article{Bloom2006,
  Title                    = {Protein stability promotes evolvability.},
  Author                   = {Jesse D Bloom and Sy T Labthavikul and Christopher R Otey and Frances H Arnold},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2006},

  Month                    = {Apr},
  Number                   = {15},
  Pages                    = {5869--5874},
  Volume                   = {103},

  Abstract                 = {The biophysical properties that enable proteins to so readily evolve to perform diverse biochemical tasks are largely unknown. Here, we show that a protein's capacity to evolve is enhanced by the mutational robustness conferred by extra stability. We use simulations with model lattice proteins to demonstrate how extra stability increases evolvability by allowing a protein to accept a wider range of beneficial mutations while still folding to its native structure. We confirm this view experimentally by mutating marginally stable and thermostable variants of cytochrome P450 BM3. Mutants of the stabilized parent were more likely to exhibit new or improved functions. Only the stabilized P450 parent could tolerate the highly destabilizing mutations needed to confer novel activities such as hydroxylating the antiinflammatory drug naproxen. Our work establishes a crucial link between protein stability and evolution. We show that we can exploit this link to discover protein functions, 
and we suggest how natural evolution might do the same.},
  Institution              = {Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA. jesse.bloom@gmail.com},
  Keywords                 = {Base Pairing; Base Sequence; Cytochrome P-450 Enzyme System, chemistry/genetics/metabolism; DNA Primers; Evolution, Molecular; Frameshift Mutation; Kinetics; Models, Molecular; Mutation; Protein Conformation; Proteins, chemistry/genetics; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {0510098103},
  Pmid                     = {16581913},
  Timestamp                = {2011.09.28}
}

@Article{Bloom2007,
  Title                    = {Evolution favors protein mutational robustness in sufficiently large populations},
  Author                   = {Bloom, Jesse D and Lu, Zhongyi and Chen, David and Raval, Alpan and Venturelli, Ophelia S and Arnold, Frances H},
  Journal                  = {BMC biology},
  Year                     = {2007},
  Number                   = {1},
  Pages                    = {29},
  Volume                   = {5},

  Owner                    = {ranjan},
  Publisher                = {BioMed Central Ltd},
  Timestamp                = {2013.11.30}
}

@Article{Bloom2007b,
  Title                    = {Thermodynamics of neutral protein evolution},
  Author                   = {Bloom, Jesse D and Raval, Alpan and Wilke, Claus O},
  Journal                  = {Genetics},
  Year                     = {2007},
  Number                   = {1},
  Pages                    = {255--266},
  Volume                   = {175},

  Owner                    = {ranjan},
  Publisher                = {Genetics Soc America},
  Timestamp                = {2013.12.02}
}

@Article{Bloom2007a,
  Title                    = {Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution},
  Author                   = {Bloom, Jesse D and Romero, Philip A and Lu, Zhongyi and Arnold, Frances H},
  Journal                  = {Biol Direct},
  Year                     = {2007},
  Pages                    = {17},
  Volume                   = {2},

  Owner                    = {ranjan},
  Timestamp                = {2013.11.30}
}

@Article{Blum1992,
  Title                    = {Scientists in open war over ``neutral theory'' of genetics},
  Author                   = {Blum, D},
  Journal                  = {Sacramento Bee},
  Year                     = {1992},
  Pages                    = {A1},

  Owner                    = {ranjan},
  Timestamp                = {2013.12.01}
}

@Article{Bolon2001a,
  Title                    = {Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity.},
  Author                   = {D. N. Bolon and S. L. Mayo},
  Journal                  = {Biochemistry},
  Year                     = {2001},

  Month                    = {Aug},
  Number                   = {34},
  Pages                    = {10047--10053},
  Volume                   = {40},

  Abstract                 = {Most globular proteins contain a core of hydrophobic residues that are inaccessible to solvent in the folded state. In general, polar residues in the core are thermodynamically unfavorable except when they are able to form intramolecular hydrogen bonds. Compared to hydrophobic interactions, polar interactions are more directional in character and may aid in fold specificity. In a survey of 263 globular protein structures, we found a strong positive correlation between the number of polar residues at core positions and protein size. To probe the importance of buried polar residues, we experimentally tested the effects of hydrophobic mutations at the five polar core residues in Escherichia coli thioredoxin. Proteins with single hydrophobic mutations (D26I, C32A, C35A, T66L, and T77V) all have cooperative unfolding transitions like the wild type (wt), as determined by chemical denaturation. Relative to wt, D26I is more stable while the other point mutants are less stable. The 
combined 5-fold mutant protein (IAALV) is less stable than wt and has an unfolding transition that is substantially less cooperative than that of wt. NMR spectra as well as amide deuterium exchange indicate that IAALV is likely sampling a number of low-energy structures in the folded state, suggesting that polar residues in the core are important for specifying a well-folded native structure.},
  Institution              = {Biochemistry Option, California Institute of Technology, Mail Code 147-75, Pasadena, California 91125, USA.},
  Keywords                 = {Amino Acid Sequence; Amino Acid Substitution; Calorimetry, Differential Scanning; Circular Dichroism; Computer Simulation; Escherichia coli, metabolism; Hydrogen Bonding; Models, Molecular; Mutagenesis, Site-Directed; Nuclear Magnetic Resonance, Biomolecular; Protein Folding; Protein Structure, Secondary; Recombinant Proteins, chemistry/metabolism; Spectrometry, Fluorescence; Thioredoxins, chemistry/metabolism},
  Owner                    = {ranjan},
  Pii                      = {bi010427y},
  Pmid                     = {11513583},
  Timestamp                = {2010.09.22}
}

@Article{Bolon2002,
  Title                    = {De novo design of biocatalysts.},
  Author                   = {Daniel N Bolon and Christopher A Voigt and Stephen L Mayo},
  Journal                  = {Curr Opin Chem Biol},
  Year                     = {2002},

  Month                    = {Apr},
  Number                   = {2},
  Pages                    = {125--129},
  Volume                   = {6},

  Abstract                 = {The challenging field of de novo enzyme design is beginning to produce exciting results. The application of powerful computational methods to functional protein design has recently succeeded at engineering target activities. In addition, efforts in directed evolution continue to expand the transformations that can be accomplished by existing enzymes. The engineering of completely novel catalytic activity requires traversing inactive sequence space in a fitness landscape, a feat that is better suited to computational design. Optimizing activity, which can include subtle alterations in backbone conformation and protein motion, is better suited to directed evolution, which is highly effective at scaling fitness landscapes towards maxima. Improved rational design efforts coupled with directed evolution should dramatically improve the scope of de novo enzyme design.},
  File                     = {Bolon2002.pdf:pdfs/Bolon2002.pdf:PDF},
  Institution              = {Biochemistry and Molecular Biophysics Option, California Institute of Technology, mail code 147-75, Pasadena, California 91125, USA.},
  Keywords                 = {Antibodies, Catalytic; Catalysis; Computer Simulation; Directed Molecular Evolution; Drug Design; Enzymes, chemical synthesis; Molecular Mimicry},
  Owner                    = {ranjan},
  Pii                      = {S1367593102003034},
  Pmid                     = {12038994},
  Timestamp                = {2010.03.11}
}

@Article{Bornberg-Bauer2010,
  Title                    = {How do new proteins arise?},
  Author                   = {Erich Bornberg-Bauer and Ann-Kathrin Huylmans and Tobias Sikosek},
  Journal                  = {Curr Op St Biol},
  Year                     = {2010},
  Pages                    = {390},
  Volume                   = {20},

  Owner                    = {ranjan},
  Timestamp                = {2010.09.02}
}

@Article{Bourne2006,
  Title                    = {Global structural changes in hepatitis B virus capsids induced by the assembly effector HAP1.},
  Author                   = {Bourne, C. R. and Finn, M. G. and Zlotnick, A.},
  Journal                  = {J Virol.},
  Year                     = {2006},
  Number                   = {22},
  Pages                    = {11055--11061},
  Volume                   = {80},

  File                     = {Bourne2006.pdf:pdfs/Bourne2006.pdf:PDF}
}

@Article{Boussau2008,
  Title                    = {Parallel adaptations to high temperatures in the Archaean eon},
  Author                   = {B. Boussau and S. Blanquart and A. Necsulea, N. Lartillot and M. Gouy},
  Journal                  = {Nature},
  Year                     = {2008},
  Pages                    = {942--945},
  Volume                   = {456},

  File                     = {Boussau2008.pdf:pdfs/Boussau2008.pdf:PDF},
  Owner                    = {ranjan},
  Timestamp                = {2010.08.24}
}

@Article{Boussau2010,
  Title                    = {Genomes as documents of evolutionary history.},
  Author                   = {Boussau, Bastien and Daubin, Vincent},
  Journal                  = {Trends Ecol Evol},
  Year                     = {2010},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {224--232},
  Volume                   = {25},

  Abstract                 = {Genomes conceal a vast intricate record of their carriers' descent and evolution. To disclose this information, biologists need phylogenetic models that integrate various levels of organization, ranging from nucleotide sequences to ecological interactions. Rates of duplication and horizontal gene transfer, organism trees and ancestral population sizes can all be inferred through statistical models of gene family evolution and population genetics. Similarly, phylogenomics combined with other fields of natural sciences can reveal the nature of ancient phenotypes and paleoenvironments. These computationally intensive approaches now benefit from progress in statistics and algorithmics. In this article, we review the recent advances and discuss possible developments towards a comprehensive reconstruction of the history of life.},
  Doi                      = {10.1016/j.tree.2009.09.007},
  Institution              = {Université de Lyon, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France.},
  Keywords                 = {Animals; Evolution, Molecular; Genetic Variation; Genome; Genomics, methods; Humans; Phylogeny},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0169-5347(09)00297-3},
  Pmid                     = {19880211},
  Timestamp                = {2014.05.18}
}

@Article{Bragg1950,
  Title                    = {Polypeptide chain configurations in crystalline proteins},
  Author                   = {Bragg, Lawrence and Kendrew, John C and Perutz, Max F},
  Journal                  = {Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences},
  Year                     = {1950},
  Number                   = {1074},
  Pages                    = {321--357},
  Volume                   = {203},

  Owner                    = {ranjan},
  Publisher                = {The Royal Society},
  Timestamp                = {2013.11.11}
}

@Book{Branden1999,
  Title                    = {Introduction to protein structure},
  Author                   = {Branden, Carl Ivar and others},
  Publisher                = {Garland Science},
  Year                     = {1999},

  Owner                    = {ranjan},
  Timestamp                = {2016.06.06}
}

@Article{Brasier2006,
  Title                    = {A fresh look at the fossil evidence for early Archaean cellular life.},
  Author                   = {Brasier, Martin and McLoughlin, Nicola and Green, Owen and Wacey, David},
  Journal                  = {Philos Trans R Soc Lond B Biol Sci},
  Year                     = {2006},

  Month                    = {Jun},
  Number                   = {1470},
  Pages                    = {887--902},
  Volume                   = {361},

  Abstract                 = {The rock record provides us with unique evidence for testing models as to when and where cellular life first appeared on Earth. Its study, however, requires caution. The biogenicity of stromatolites and 'microfossils' older than 3.0 Gyr should not be accepted without critical analysis of morphospace and context, using multiple modern techniques, plus rejection of alternative non-biological (null) hypotheses. The previous view that the co-occurrence of biology-like morphology and carbonaceous chemistry in ancient, microfossil-like objects is a presumptive indicator of biogenicity is not enough. As with the famous Martian microfossils, we need to ask not 'what do these structures remind us of?', but 'what are these structures?' Earth's oldest putative 'microfossil' assemblages within 3.4-3.5 Gyr carbonaceous cherts, such as the Apex Chert, are likewise self-organizing structures that do not pass tests for biogenicity. There is a preservational paradox in the fossil record prior to 
ca 2.7 Gyr: suitable rocks (e.g. isotopically light carbonaceous cherts) are widely present, but signals of life are enigmatic and hard to decipher. One new approach includes detailed mapping of well-preserved sandstone grains in the ca 3.4 Gyr Strelley Pool Chert. These can contain endolithic microtubes showing syngenicity, grain selectivity and several levels of geochemical processing. Preliminary studies invite comparison with a class of ambient inclusion trails of putative microbial origin and with the activities of modern anaerobic proteobacteria and volcanic glass euendoliths.},
  Institution              = {Oxford University, Department of Earth Sciences, Parks Road, Oxford OX1 3PR, UK. martinb@earth.ox.ac.uk},
  Keywords                 = {Biogenesis; Environment; Fossils; Geologic Sediments, microbiology; Morphogenesis; Western Australia},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {G8G813455W76LV45},
  Pmid                     = {16754605},
  Timestamp                = {2012.04.06}
}

@Article{Breinl1930,
  Title                    = {Chemische Untersuchung des Pr{\"a}zipitates aus H{\"a}moglobin und Anti-H{\"a}moglobin-Serum und Bemerkungen {\"u}ber die Natur der Antik{\"o}rper.},
  Author                   = {Breinl, Friedrich and Haurowitz, Felix},
  Journal                  = {Hoppe-Seyler{\'{}} s Zeitschrift f{\"u}r physiologische Chemie},
  Year                     = {1930},
  Number                   = {1-3},
  Pages                    = {45--57},
  Volume                   = {192},

  Owner                    = {ranjan},
  Timestamp                = {2013.12.03}
}

@Article{Bridgham2006,
  Title                    = {Evolution of hormone-receptor complexity by molecular exploitation.},
  Author                   = {Jamie T Bridgham and Sean M Carroll and Joseph W Thornton},
  Journal                  = {Science},
  Year                     = {2006},

  Month                    = {Apr},
  Number                   = {5770},
  Pages                    = {97--101},
  Volume                   = {312},

  Abstract                 = {According to Darwinian theory, complexity evolves by a stepwise process of elaboration and optimization under natural selection. Biological systems composed of tightly integrated parts seem to challenge this view, because it is not obvious how any element's function can be selected for unless the partners with which it interacts are already present. Here we demonstrate how an integrated molecular system-the specific functional interaction between the steroid hormone aldosterone and its partner the mineralocorticoid receptor-evolved by a stepwise Darwinian process. Using ancestral gene resurrection, we show that, long before the hormone evolved, the receptor's affinity for aldosterone was present as a structural by-product of its partnership with chemically similar, more ancient ligands. Introducing two amino acid changes into the ancestral sequence recapitulates the evolution of present-day receptor specificity. Our results indicate that tight interactions can evolve by 
molecular exploitation-recruitment of an older molecule, previously constrained for a different role, into a new functional complex.},
  Institution              = {Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA.},
  Keywords                 = {Aldosterone, chemistry/metabolism; Amino Acid Substitution; Animals; Bayes Theorem; Binding Sites; Desoxycorticosterone, metabolism; Evolution, Molecular; Gene Duplication; Hagfishes; Hydrocortisone, metabolism; Lampreys; Ligands; Mutation; Perciformes; Phylogeny; Rats; Receptors, Aldosterone, genetics/metabolism; Receptors, Glucocorticoid, chemistry/genetics/metabolism; Receptors, Mineralocorticoid, chemistry/genetics/metabolism; Receptors, Steroid, chemistry/genetics/metabolism; Skates (Fish)},
  Owner                    = {ranjan},
  Pii                      = {312/5770/97},
  Pmid                     = {16601189},
  Timestamp                = {2010.04.20}
}

@Article{Bridgham2009,
  Title                    = {An epistatic ratchet constrains the direction of glucocorticoid receptor evolution.},
  Author                   = {Jamie T Bridgham and Eric A Ortlund and Joseph W Thornton},
  Journal                  = {Nature},
  Year                     = {2009},

  Month                    = {Sep},
  Number                   = {7263},
  Pages                    = {515--519},
  Volume                   = {461},

  Abstract                 = {The extent to which evolution is reversible has long fascinated biologists. Most previous work on the reversibility of morphological and life-history evolution has been indecisive, because of uncertainty and bias in the methods used to infer ancestral states for such characters. Further, despite theoretical work on the factors that could contribute to irreversibility, there is little empirical evidence on its causes, because sufficient understanding of the mechanistic basis for the evolution of new or ancestral phenotypes is seldom available. By studying the reversibility of evolutionary changes in protein structure and function, these limitations can be overcome. Here we show, using the evolution of hormone specificity in the vertebrate glucocorticoid receptor as a case-study, that the evolutionary path by which this protein acquired its new function soon became inaccessible to reverse exploration. Using ancestral gene reconstruction, protein engineering and X-ray 
crystallography, we demonstrate that five subsequent 'restrictive' mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key function-switching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.},
  Institution              = {Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403, USA.},
  Keywords                 = {Animals; CHO Cells; Cricetinae; Cricetulus; Crystallography, X-Ray; Epistasis, Genetic; Evolution, Molecular; Hormones, metabolism; Models, Biological; Models, Molecular; Mutation, genetics; Protein Engineering; Receptors, Glucocorticoid, chemistry/genetics/metabolism; Sequence Alignment; Substrate Specificity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nature08249},
  Pmid                     = {19779450},
  Timestamp                = {2011.09.15}
}

@InProceedings{Broadbent1957,
  Title                    = {Percolation processes I. Crystals and mazes},
  Author                   = {Broadbent, Simon R and Hammersley, John M},
  Booktitle                = {Proc. Cambridge Philos. Soc},
  Year                     = {1957},
  Number                   = {3},
  Pages                    = {629--41},
  Volume                   = {53},

  Owner                    = {ranjan},
  Timestamp                = {2013.07.06}
}

@Article{Brocchieri2005,
  Title                    = {Protein length in eukaryotic and prokaryotic proteomes.},
  Author                   = {Brocchieri, Luciano and Karlin, Samuel},
  Journal                  = {Nucleic Acids Res},
  Year                     = {2005},
  Number                   = {10},
  Pages                    = {3390--3400},
  Volume                   = {33},

  Abstract                 = {We analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. Comparing Eukaryotes and Prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. The magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended multi-functional and multi-domain proteins. Comparing Bacteria and Archaea, we determined that the small but significant length difference observed between their proteins results from a combination of three factors: (i) bacterial proteomes include a greater proportion than archaeal proteomes of longer proteins involved in metabolism or cellular processes, (ii) within most functional classes, protein families unique to Bacteria are generally longer than protein families unique to Archaea 
and (iii) within the same protein family, homologs from Bacteria tend to be longer than the corresponding homologs from Archaea. These differences are interpreted with respect to evolutionary trends and prevailing environmental conditions within the two prokaryotic groups.},
  Doi                      = {10.1093/nar/gki615},
  Institution              = {Department of Mathematics, Stanford University Stanford, CA 94305-2125, USA.},
  Keywords                 = {Amino Acid Sequence; Animals; Archaeal Proteins, chemistry/classification; Bacterial Proteins, chemistry/classification; Eukaryotic Cells, metabolism; Evolution, Molecular; Humans; Protein Structure, Tertiary; Proteome, chemistry/classification; Proteomics},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {33/10/3390},
  Pmid                     = {15951512},
  Timestamp                = {2014.02.24}
}

@Article{Bromham2003,
  Title                    = {Molecular clocks and explosive radiations.},
  Author                   = {Lindell Bromham},
  Journal                  = {J Mol Evol},
  Year                     = {2003},
  Pages                    = {S13--S20},
  Volume                   = {57 Suppl 1},

  Abstract                 = {Molecular data are ideal for exploring evolutionary history because of its universality, stochasticity, and abundance. These features provide a means of exploring the evolutionary history of all organisms (including those that do not tend to leave fossils), potentially within a statistical framework that allows testing of evolutionary hypotheses. However, the discrepancy between molecular and paleontological dates for three key "explosive" radiations inferred from the fossil record--the Cambrian explosion of animal phyla and the post-KT radiations of modern orders of mammals and birds--have led to a reexamination of the assumptions on which molecular dates are based. Could variation in the rate of molecular evolution, perhaps associated with "explosive" radiations, cause overestimation of diversification dates? Here I examine four hypothetical causes of fast molecular rates in explosive radiations--body size, morphological rate, speciation rate, and ecological diversification--
using available empirical evidence on patterns of variation in rate of molecular evolution.},
  Institution              = {Biological Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK. L.D.Bromham@sussex.ac.uk},
  Keywords                 = {Animals; Biological Evolution; Birds, physiology; Body Constitution; Evolution, Molecular; Fossils; Mammals, physiology; Primates, physiology; Radiation; Species Specificity; Time},
  Owner                    = {ranjan},
  Pmid                     = {15008399},
  Timestamp                = {2011.04.26}
}

@Article{Bromham2003a,
  Title                    = {The modern molecular clock},
  Author                   = {Bromham, Lindell and Penny, David},
  Journal                  = {Nature Reviews Genetics},
  Year                     = {2003},
  Number                   = {3},
  Pages                    = {216--224},
  Volume                   = {4},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2013.12.02}
}

@Article{Brooks2009,
  Title                    = {CHARMM: the biomolecular simulation program.},
  Author                   = {Brooks, B. R. and Brooks, 3rd, CL and Mackerell, Jr, AD and Nilsson, L. and Petrella, R. J. and Roux, B. and Won, Y. and Archontis, G. and Bartels, C. and Boresch, S. and Caflisch, A. and Caves, L. and Cui, Q. and Dinner, A. R. and Feig, M. and Fischer, S. and Gao, J. and Hodoscek, M. and Im, W. and Kuczera, K. and Lazaridis, T. and Ma, J. and Ovchinnikov, V. and Paci, E. and Pastor, R. W. and Post, C. B. and Pu, J. Z. and Schaefer, M. and Tidor, B. and Venable, R. M. and Woodcock, H. L. and Wu, X. and Yang, W. and York, D. M. and Karplus, M.},
  Journal                  = {J Comput Chem},
  Year                     = {2009},

  Month                    = {Jul},
  Number                   = {10},
  Pages                    = {1545--1614},
  Volume                   = {30},

  Abstract                 = {CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent 
and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.},
  Institution              = {Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. brbrooks@helix.nih.gov},
  Keywords                 = {Carbohydrates, chemistry; Computational Biology; Computer Simulation; Lipids, chemistry; Models, Chemical; Models, Molecular; Nucleic Acids, chemistry; Peptides, chemistry; Proteins, chemistry; Quantum Theory; Software},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {19444816},
  Timestamp                = {2012.06.21}
}

@Article{Brower2004,
  Title                    = {Comment on ``Molecular phylogenies link rates of evolution and speciation'' (II).},
  Author                   = {Andrew V Z Brower},
  Journal                  = {Science},
  Year                     = {2004},

  Month                    = {Jan},
  Number                   = {5655},
  Pages                    = {173c},
  Volume                   = {303},

  Institution              = {Department of Zoology, Oregon State University, Corvallis, OR 97331, USA. browera@science.oregonstate.edu},
  Keywords                 = {Animals; Biological Evolution; Evolution, Molecular; Genes; Mathematics; Models, Statistical; Phylogeny; Sampling Studies},
  Owner                    = {ranjan},
  Pii                      = {303/5655/173c},
  Pmid                     = {14715995},
  Timestamp                = {2011.04.26}
}

@Article{Brown2001,
  Title                    = {Universal trees based on large combined protein sequence data sets.},
  Author                   = {Brown, J. R. and Douady, C. J. and Italia, M. J. and Marshall, W. E. and Stanhope, M. J.},
  Journal                  = {Nat Genet},
  Year                     = {2001},

  Month                    = {Jul},
  Number                   = {3},
  Pages                    = {281--285},
  Volume                   = {28},

  Abstract                 = {Universal trees of life based on small-subunit (SSU) ribosomal RNA (rRNA) support the separate mono/holophyly of the domains Archaea (archaebacteria), Bacteria (eubacteria) and Eucarya (eukaryotes) and the placement of extreme thermophiles at the base of the Bacteria. The concept of universal tree reconstruction recently has been upset by protein trees that show intermixing of species from different domains. Such tree topologies have been attributed to either extensive horizontal gene transfer or degradation of phylogenetic signals because of saturation for amino acid substitutions. Here we use large combined alignments of 23 orthologous proteins conserved across 45 species from all domains to construct highly robust universal trees. Although individual protein trees are variable in their support of domain integrity, trees based on combined protein data sets strongly support separate monophyletic domains. Within the Bacteria, we placed spirochaetes as the earliest derived 
bacterial group. However, elimination from the combined protein alignment of nine protein data sets, which were likely candidates for horizontal gene transfer, resulted in trees showing thermophiles as the earliest evolved bacterial lineage. Thus, combined protein universal trees are highly congruent with SSU rRNA trees in their strong support for the separate monophyly of domains as well as the early evolution of thermophilic Bacteria.},
  Institution              = {Anti-Microbial Bioinformatics Group, GlaxoSmithKline,1250 South Collegeville Road, UP1345 P.O. Box 5089, Collegeville, Pennsylvania 19426-0989, USA. James_R_Brown@gsk.com},
  Keywords                 = {Amino Acid Sequence; Archaea, genetics; Bacteria, genetics; Conserved Sequence; Databases, Factual; Eukaryotic Cells; Evolution, Molecular; Genomics; Phylogeny; Sequence Alignment; Sequence Analysis, Protein, methods},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {90129},
  Pmid                     = {11431701},
  Timestamp                = {2012.09.06}
}

@Article{Brumer2006,
  Title                    = {Genetic instability and the quasispecies model.},
  Author                   = {Yisroel Brumer and Franziska Michor and Eugene I Shakhnovich},
  Journal                  = {J Theor Biol},
  Year                     = {2006},

  Month                    = {Jul},
  Number                   = {2},
  Pages                    = {216--222},
  Volume                   = {241},

  Abstract                 = {Genetic instability is a defining characteristic of cancers. Microsatellite instability (MIN) leads to by elevated point mutation rates, whereas chromosomal instability (CIN) refers to increased rates of losing or gaining whole chromosomes or parts of chromosomes during cell division. CIN and MIN are, in general, mutually exclusive. The quasispecies model is a very successful theoretical framework for the study of evolution at high mutation rates. It predicts the existence of an experimentally verified error catastrophe. This catastrophe occurs when the mutation rates exceed a threshold value, the error threshold, above which replicative infidelity is incompatible with cell survival. We analyse the semiconservative quasispecies model of both MIN and CIN tumors. We consider the role of post-methylation DNA repair in tumor cells and demonstrate that DNA repair is fundamental to the nature of the error catastrophe in both types of tumors. We find that CIN introduces a plateau in 
the maximum viable mutation rate for a repair-free model, which does not exist in the case of MIN. This provides a plausible explanation for the mutual exclusivity of CIN and MIN.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. brumer@post.harvard.edu},
  Keywords                 = {Chromosomal Instability; DNA Methylation; DNA Repair; DNA, Neoplasm, genetics; Genome; Humans; Microsatellite Instability; Models, Genetic; Neoplasms, genetics},
  Owner                    = {ranjan},
  Pii                      = {S0022-5193(05)00504-7},
  Pmid                     = {16386760},
  Timestamp                = {2009.12.05}
}

@Article{Brumer2005,
  Title                    = {Selective advantage for conservative viruses.},
  Author                   = {Yisroel Brumer and Eugene I Shakhnovich},
  Journal                  = {Phys Rev E Stat Nonlin Soft Matter Phys},
  Year                     = {2005},

  Month                    = {Mar},
  Number                   = {3 Pt 1},
  Pages                    = {031903},
  Volume                   = {71},

  Abstract                 = {In this article we study the full semiconservative treatment of a model for the coevolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semiconservatively replicating viruses interacting with a realistic semiconservatively replicating immune system. The conservative virus is found to have a selective advantage in the form of an ability to survive in regions with a wider range of mutation rates than its semiconservative counterpart, as well as an increased replication rate where both species can survive. This may help explain the existence of a rich range of viruses with conservatively replicating genomes, a trait that is found nowhere else in nature.},
  Institution              = {Harvard University, Cambridge, Massachusetts 02138, USA.},
  Keywords                 = {Adaptation, Physiological, immunology; Animals; Evolution; Host-Parasite Interactions, immunology; Humans; Immune System, immunology/virology; Immunity, Innate, immunology; Models, Biological; Selection (Genetics); Virus Replication, physiology; Viruses, genetics/immunology},
  Owner                    = {ranjan},
  Pmid                     = {15903455},
  Timestamp                = {2009.12.05}
}

@Article{Brumer2004,
  Title                    = {Importance of DNA repair in tumor suppression.},
  Author                   = {Yisroel Brumer and Eugene I Shakhnovich},
  Journal                  = {Phys Rev E Stat Nonlin Soft Matter Phys},
  Year                     = {2004},

  Month                    = {Dec},
  Number                   = {6 Pt 1},
  Pages                    = {061912},
  Volume                   = {70},

  Abstract                 = {The transition from a normal to cancerous cell requires a number of highly specific mutations that affect cell cycle regulation, apoptosis, differentiation, and many other cell functions. One hallmark of cancerous genomes is genomic instability, with mutation rates far greater than those of normal cells. In microsatellite instability (MIN tumors), these are often caused by damage to mismatch repair genes, allowing further mutation of the genome and tumor progression. These mutation rates may lie near the error catastrophe found in the quasispecies model of adaptive RNA genomes, suggesting that further increasing mutation rates will destroy cancerous genomes. However, recent results have demonstrated that DNA genomes exhibit an error threshold at mutation rates far lower than their conservative counterparts. Furthermore, while the maximum viable mutation rate in conservative systems increases indefinitely with increasing master sequence fitness, the semiconservative threshold 
plateaus at a relatively low value. This implies a paradox, wherein inaccessible mutation rates are found in viable tumor cells. In this paper, we address this paradox, demonstrating an isomorphism between the conservatively replicating (RNA) quasispecies model and the semiconservative (DNA) model with post-methylation DNA repair mechanisms impaired. Thus, as DNA repair becomes inactivated, the maximum viable mutation rate increases smoothly to that of a conservatively replicating system on a transformed landscape, with an upper bound that is dependent on replication rates. On a specific single fitness peak landscape, the repair-free semiconservative system is shown to mimic a conservative system exactly. We postulate that inactivation of post-methylation repair mechanisms is fundamental to the progression of a tumor cell and hence these mechanisms act as a method for the prevention and destruction of cancerous genomes.},
  Institution              = {Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.},
  Keywords                 = {Animals; Base Pair Mismatch, genetics; Computer Simulation; DNA Damage, genetics; DNA Mutational Analysis, methods; DNA Repair, genetics; DNA Replication, genetics; DNA, Neoplasm, genetics; Evolution, Molecular; Genetic Variation, genetics; Genetics, Population; Models, Genetic; Neoplasms, genetics; Sequence Analysis, DNA, methods; Suppression, Genetic, genetics},
  Owner                    = {ranjan},
  Pmid                     = {15697407},
  Timestamp                = {2009.12.05}
}

@Article{Brumer2004a,
  Title                    = {Host-parasite coevolution and optimal mutation rates for semiconservative quasispecies.},
  Author                   = {Yisroel Brumer and Eugene I Shakhnovich},
  Journal                  = {Phys Rev E Stat Nonlin Soft Matter Phys},
  Year                     = {2004},

  Month                    = {Jun},
  Number                   = {6 Pt 1},
  Pages                    = {061909},
  Volume                   = {69},

  Abstract                 = {In this paper, we extend a model of host-parasite coevolution to incorporate the semiconservative nature of DNA replication for both the host and the parasite. We find that the optimal mutation rate for the semiconservative and conservative hosts converge for realistic genome lengths, thus maintaining the admirable agreement between theory and experiment found previously for the conservative model and justifying the conservative approximation in some cases. We demonstrate that, while the optimal mutation rate for a conservative and semiconservative parasite interacting with a given immune system is similar to that of a conservative parasite, the properties away from this optimum differ significantly. We suspect that this difference, coupled with the requirement that a parasite optimize survival in a range of viable hosts, may help explain why semiconservative viruses are known to have significantly lower mutation rates than their conservative counterparts.},
  Institution              = {Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.},
  Keywords                 = {Adaptation, Physiological, genetics; Animals; Competitive Behavior, physiology; Computer Simulation; Ecosystem; Evolution; Food Chain; Genetics, Population; Homeostasis, genetics; Host-Parasite Interactions, genetics; Humans; Immune System, immunology/virology; Models, Genetic; Models, Statistical; Mutation, genetics; Population Dynamics; Population Growth; Predatory Behavior, physiology; Selection (Genetics); Survival; Survival Analysis; Viruses, genetics/immunology},
  Owner                    = {ranjan},
  Pmid                     = {15244619},
  Timestamp                = {2009.12.05}
}

@Article{Bryngelson1995,
  Title                    = {Funnels, pathways, and the energy landscape of protein folding: a synthesis},
  Author                   = {Bryngelson, Joseph D and Onuchic, Jose Nelson and Socci, Nicholas D and Wolynes, Peter G},
  Journal                  = {Proteins: Structure, Function, and Bioinformatics},
  Year                     = {1995},
  Number                   = {3},
  Pages                    = {167--195},
  Volume                   = {21},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2014.09.02}
}

@Article{Bryngelson1987,
  Title                    = {Spin glasses and the statistical mechanics of protein folding.},
  Author                   = {J. D. Bryngelson and P. G. Wolynes},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1987},

  Month                    = {Nov},
  Number                   = {21},
  Pages                    = {7524--7528},
  Volume                   = {84},

  Abstract                 = {The theory of spin glasses was used to study a simple model of protein folding. The phase diagram of the model was calculated, and the results of dynamics calculations are briefly reported. The relation of these results to folding experiments, the relation of these hypotheses to previous protein folding theories, and the implication of these hypotheses for protein folding prediction schemes are discussed.},
  Institution              = {Noyes Laboratory, University of Illinois, Urbana 61801.},
  Keywords                 = {Kinetics; Mathematics; Models, Theoretical; Protein Conformation; Proteins; Stochastic Processes},
  Owner                    = {ranjan},
  Pmid                     = {3478708},
  Timestamp                = {2010.01.20}
}

@Article{Butterfoss2009,
  Title                    = {A preliminary survey of the peptoid folding landscape},
  Author                   = {Butterfoss, Glenn L and Renfrew, P Douglas and Kuhlman, Brian and Kirshenbaum, Kent and Bonneau, Richard},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {2009},
  Number                   = {46},
  Pages                    = {16798--16807},
  Volume                   = {131},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2014.06.11}
}

@Article{Butterfoss2012,
  Title                    = {De novo structure prediction and experimental characterization of folded peptoid oligomers},
  Author                   = {Butterfoss, Glenn L and Yoo, Barney and Jaworski, Jonathan N and Chorny, Ilya and Dill, Ken A and Zuckermann, Ronald N and Bonneau, Richard and Kirshenbaum, Kent and Voelz, Vincent A},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2012},
  Number                   = {36},
  Pages                    = {14320--14325},
  Volume                   = {109},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2014.08.25}
}

@Article{Caetano-Anolles2003,
  Title                    = {An evolutionarily structured universe of protein architecture.},
  Author                   = {Gustavo Caetano-Anoll\'{e}s and Derek Caetano-Anoll\'{e}s},
  Journal                  = {Genome Res},
  Year                     = {2003},

  Month                    = {Jul},
  Number                   = {7},
  Pages                    = {1563--1571},
  Volume                   = {13},

  Abstract                 = {Protein structural diversity encompasses a finite set of architectural designs. Embedded in these topologies are evolutionary histories that we here uncover using cladistic principles and measurements of protein-fold usage and sharing. The reconstructed phylogenies are inherently rooted and depict histories of protein and proteome diversification. Proteome phylogenies showed two monophyletic sister-groups delimiting Bacteria and Archaea, and a topology rooted in Eucarya. This suggests three dramatic evolutionary events and a common ancestor with a eukaryotic-like, gene-rich, and relatively modern organization. Conversely, a general phylogeny of protein architectures showed that structural classes of globular proteins appeared early in evolution and in defined order, the alpha/beta class being the first. Although most ancestral folds shared a common architecture of barrels or interleaved beta-sheets and alpha-helices, many were clearly derived, such as polyhedral folds in the all-
alpha class and beta-sandwiches, beta-propellers, and beta-prisms in all-beta proteins. We also describe transformation pathways of architectures that are prevalently used in nature. For example, beta-barrels with increased curl and stagger were favored evolutionary outcomes in the all-beta class. Interestingly, we found cases where structural change followed the alpha-to-beta tendency uncovered in the tree of architectures. Lastly, we traced the total number of enzymatic functions associated with folds in the trees and show that there is a general link between structure and enzymatic function.},
  File                     = {Caetano-Anolles2003.pdf:pdfs/Caetano-Anolles2003.pdf:PDF},
  Institution              = {Vital NRG, Knoxville, Tennessee 37919, USA. gca@uiuc.edu},
  Keywords                 = {Animals; Catalytic Domain, genetics; Computational Biology, methods/statistics /&/ numerical data; Databases, Protein, statistics /&/ numerical data; Enzymes, chemistry/genetics/metabolism; Evolution, Molecular; Phylogeny; Protein Conformation; Protein Folding; Protein Structure, Tertiary, genetics; Proteins, chemistry/genetics/metabolism; Proteome, chemistry/genetics/metabolism},
  Owner                    = {ranjan},
  Pii                      = {13/7/1563},
  Pmid                     = {12840035},
  Timestamp                = {2009.09.11}
}

@Article{Caetano-Anolles2009,
  Title                    = {The origin, evolution and structure of the protein world.},
  Author                   = {Gustavo Caetano-Anoll\'{e}s and Minglei Wang and Derek Caetano-Anoll\'{e}s and Jay E Mittenthal},
  Journal                  = {Biochem J},
  Year                     = {2009},

  Month                    = {Feb},
  Number                   = {3},
  Pages                    = {621--637},
  Volume                   = {417},

  Abstract                 = {Contemporary protein architectures can be regarded as molecular fossils, historical imprints that mark important milestones in the history of life. Whereas sequences change at a considerable pace, higher-order structures are constrained by the energetic landscape of protein folding, the exploration of sequence and structure space, and complex interactions mediated by the proteostasis and proteolytic machineries of the cell. The survey of architectures in the living world that was fuelled by recent structural genomic initiatives has been summarized in protein classification schemes, and the overall structure of fold space explored with novel bioinformatic approaches. However, metrics of general structural comparison have not yet unified architectural complexity using the 'shared and derived' tenet of evolutionary analysis. In contrast, a shift of focus from molecules to proteomes and a census of protein structure in fully sequenced genomes were able to uncover global evolutionary 
patterns in the structure of proteins. Timelines of discovery of architectures and functions unfolded episodes of specialization, reductive evolutionary tendencies of architectural repertoires in proteomes and the rise of modularity in the protein world. They revealed a biologically complex ancestral proteome and the early origin of the archaeal lineage. Studies also identified an origin of the protein world in enzymes of nucleotide metabolism harbouring the P-loop-containing triphosphate hydrolase fold and the explosive discovery of metabolic functions that recapitulated well-defined prebiotic shells and involved the recruitment of structures and functions. These observations have important implications for origins of modern biochemistry and diversification of life.},
  Institution              = {Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W. Peabody Drive, Urbana, IL 61801, USA. gca@illinois.edu},
  Keywords                 = {Animals; Evolution, Molecular; Genomics; Humans; Models, Molecular; Phylogeny; Protein Conformation; Protein Folding; Proteins, chemistry/genetics; Proteome, chemistry/genetics; Structure-Activity Relationship},
  Owner                    = {ranjan},
  Pii                      = {BJ20082063},
  Pmid                     = {19133840},
  Timestamp                = {2010.02.06}
}

@Article{Cairns-Smith1966,
  Title                    = {The origin of life and the nature of the primitive gene.},
  Author                   = {Cairns-Smith, A. G.},
  Journal                  = {J Theor Biol},
  Year                     = {1966},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {53--88},
  Volume                   = {10},

  Keywords                 = {Biogenesis; Biological Evolution; Chemical Phenomena; Chemistry; Crystallization; Genes, analysis; Macromolecular Substances; Models, Theoretical},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {0022-5193(66)90178-0},
  Pmid                     = {5964688},
  Timestamp                = {2012.04.05}
}

@Article{Camacho1993,
  Title                    = {Minimum energy compact structures of random sequences of heteropolymers.},
  Author                   = {Camacho and Thirumalai},
  Journal                  = {Phys Rev Lett},
  Year                     = {1993},

  Month                    = {Oct},
  Number                   = {15},
  Pages                    = {2505--2508},
  Volume                   = {71},

  File                     = {Camacho1993.pdf:pdfs/Camacho1993.pdf:PDF;Camacho1993a.pdf:pdfs/Camacho1993a.pdf:PDF},
  Owner                    = {ranjan},
  Pmid                     = {10054697},
  Timestamp                = {2010.01.18}
}

@Article{Camacho1993a,
  Title                    = {Kinetics and thermodynamics of folding in model proteins.},
  Author                   = {C. J. Camacho and D. Thirumalai},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1993},

  Month                    = {Jul},
  Number                   = {13},
  Pages                    = {6369--6372},
  Volume                   = {90},

  Abstract                 = {Monte Carlo simulations on a class of lattice models are used to probe the thermodynamics and kinetics of protein folding. We find two transition temperatures: one at T theta, when chains collapse from a coil to a compact phase, and the other at Tf (< T theta), when chains adopt a conformation corresponding to their native state. The kinetics are probed by several correlation functions and are interpreted in terms of the underlying energy landscape. The transition from the coil to the native state occurs in three distinct stages. The initial stage corresponds to a random collapse of the protein chain. At intermediate times tau c, during which much of the native structure is acquired, there are multiple pathways. For longer times tau r (>> tau c) the decay is exponential, suggestive of a late transition state. The folding time scale (approximately tau r) varies greatly depending on the model. Implications of our results for in vitro folding of proteins are discussed.},
  File                     = {Camacho1993a.pdf:pdfs/Camacho1993a.pdf:PDF},
  Institution              = {Institute for Physical Science and Technology, University of Maryland, College Park 20742.},
  Keywords                 = {Kinetics; Models, Chemical; Monte Carlo Method; Protein Folding; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {8327519},
  Timestamp                = {2010.01.18}
}

@Article{Campbell2006,
  Title                    = {Biochemistry, ; Thomson Brooks},
  Author                   = {Campbell, MK and Farrell, SO},
  Journal                  = {Cole, Belmont, CA},
  Year                     = {2006},

  Owner                    = {ranjan},
  Timestamp                = {2013.07.24}
}

@Article{Cantor1877,
  Title                    = {Ein Beitrag zur Mannigfaltigkeitslehre.},
  Author                   = {Cantor, Georg},
  Journal                  = {Journal f{\"u}r die reine und angewandte Mathematik},
  Year                     = {1877},
  Pages                    = {242--258},
  Volume                   = {84},

  Owner                    = {ranjan},
  Timestamp                = {2015.03.02}
}

@Article{Carrillo-Tripp2009,
  Title                    = {VIPERdb2: an enhanced and web API enabled relational database for structural virology},
  Author                   = {Carrillo-Tripp,M. and Shepherd,C.M. and Borelli,I.A. and Venkataraman,S. and Lander,G. and Natarajan,P. and Johnson,J.E. and Brooks III,C.L. and Reddy,V.S.},
  Journal                  = {Nucleic Acids Res.},
  Year                     = {2009},
  Pages                    = {D436-D442},
  Volume                   = {37}
}

@Article{Caspar1956,
  Title                    = {Structure of bushy stunt virus.},
  Author                   = {Caspar,D.L.},
  Journal                  = {Nature},
  Year                     = {1956},
  Pages                    = {475-476},
  Volume                   = {177},

  Owner                    = {ranjan},
  Timestamp                = {2009.08.14}
}

@Article{Caspar1962,
  Title                    = {Physical principles in the construction of regular viruses},
  Author                   = {Caspar, D. L. D and Klug, A.},
  Journal                  = {Cold Spring Harbor Symp.},
  Year                     = {1962},
  Pages                    = {1--24},
  Volume                   = {27},

  File                     = {Caspar1962.pdf:pdfs/Caspar1962.pdf:PDF}
}

@Article{Chan1991,
  Title                    = {Polymer principles in protein structure and stability.},
  Author                   = {H. S. Chan and K. A. Dill},
  Journal                  = {Annu Rev Biophys Biophys Chem},
  Year                     = {1991},
  Pages                    = {447--490},
  Volume                   = {20},

  File                     = {Chan1991.pdf:pdfs/Chan1991.pdf:PDF},
  Institution              = {Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204.},
  Keywords                 = {Drug Stability; Mathematics; Models, Molecular; Polymers; Protein Conformation; Proteins, chemistry; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {1867723},
  Timestamp                = {2010.01.18}
}

@Book{Chandler1987,
  Title                    = {Introduction to modern statistical mechanics},
  Author                   = {Chandler, David},
  Publisher                = {Oxford University Press},
  Year                     = {1987},
  Volume                   = {1},

  ISBN                     = {0195042778},
  Owner                    = {ranjan},
  Timestamp                = {2015.06.29}
}

@Article{Chang2008,
  Title                    = {Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association.},
  Author                   = {Chia-En A Chang and William A McLaughlin and Riccardo Baron and Wei Wang and J. Andrew McCammon},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2008},

  Month                    = {May},
  Number                   = {21},
  Pages                    = {7456--7461},
  Volume                   = {105},

  Abstract                 = {The mechanisms by which a promiscuous protein can strongly interact with several different proteins using the same binding interface are not completely understood. An example is protein kinase A (PKA), which uses a single face on its docking/dimerization domain to interact with multiple A-kinase anchoring proteins (AKAP) that localize it to different parts of the cell. In the current study, the configurational entropy contributions to the binding between the AKAP protein HT31 with the D/D domain of RII alpha-regulatory subunit of PKA were examined. The results show that the majority of configurational entropy loss for the interaction was due to decreased fluctuations within rotamer states of the side chains. The result is in contrast to the widely held approximation that the decrease in the number of rotamer states available to the side chains forms the major component. Further analysis showed that there was a direct linear relationship between total configurational entropy and 
the number of favorable, alternative contacts available within hydrophobic environments. The hydrophobic binding pocket of the D/D domain provides alternative contact points for the side chains of AKAP peptides that allow them to adopt different binding conformations. The increase in binding conformations provides an increase in binding entropy and hence binding affinity. We infer that a general strategy for a promiscuous protein is to provide alternative contact points at its interface to increase binding affinity while the plasticity required for binding to multiple partners is retained. Implications are discussed for understanding and treating diseases in which promiscuous protein interactions are used.},
  Institution              = {Departments of Chemistry and Biochemistry and Pharmacology, Center for Theoretical Biological Physics Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093-0365, USA.},
  Keywords                 = {A Kinase Anchor Proteins, chemistry; Cyclic AMP-Dependent Protein Kinase RIIalpha Subunit, chemistry; Entropy; Hydrophobicity; Peptides, chemistry; Protein Conformation},
  Owner                    = {ranjan},
  Pii                      = {0800452105},
  Pmid                     = {18495919},
  Timestamp                = {2010.02.05}
}

@Article{Chantler1995,
  Title                    = {Theoretical form factor, attenuation, and scattering tabulation for Z= 1--92 from E= 1--10 eV to E= 0.4--1.0 MeV},
  Author                   = {Chantler, CT},
  Journal                  = {Journal of Physical and Chemical Reference Data},
  Year                     = {1995},
  Number                   = {1},
  Pages                    = {71--643},
  Volume                   = {24},

  Owner                    = {ranjan},
  Publisher                = {AIP Publishing},
  Timestamp                = {2014.08.27}
}

@Article{Chebrek2014,
  Title                    = {PolyprOnline: polyproline helix II and secondary structure assignment database},
  Author                   = {Chebrek, Romain and Leonard, Sylvain and de Brevern, Alexandre G and Gelly, Jean-Christophe},
  Journal                  = {Database},
  Year                     = {2014},
  Pages                    = {bau102},
  Volume                   = {2014},

  Owner                    = {ranjan},
  Publisher                = {Oxford University Press},
  Timestamp                = {2016.02.02}
}

@Article{Chelliah2005,
  Title                    = {Quantifying structural and functional restraints on amino acid substitutions in evolution of proteins.},
  Author                   = {V. Chelliah and T. L. Blundell},
  Journal                  = {Biochemistry (Mosc)},
  Year                     = {2005},

  Month                    = {Aug},
  Number                   = {8},
  Pages                    = {835--840},
  Volume                   = {70},

  Abstract                 = {One of Oleg Ptitsyn's most important papers (Shakhnovich, E., Abkevich, V., and Ptitsyn, O. (1996) Nature, 379, 96-98) describes how knowledge of structure and function can be used to understand better the nature of amino acid substitutions in families and superfamilies of proteins. The selective advantages of retaining structure and function during evolution can be expressed as restraints on the amino acid substitutions that are accepted.},
  Institution              = {Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, England.},
  Keywords                 = {Algorithms; Amino Acid Substitution, genetics; Animals; Binding Sites, genetics; Evolution, Molecular; Humans; Protein Conformation; Proteins, chemistry/genetics; Selection (Genetics)},
  Owner                    = {ranjan},
  Pii                      = {BCM70081013},
  Pmid                     = {16212538},
  Timestamp                = {2009.12.05}
}

@Article{Chen2011a,
  Title                    = {Engineered biomimetic polymers as tunable agents for controlling CaCO3 mineralization.},
  Author                   = {Chen, Chun-Long and Qi, Jiahui and Zuckermann, Ronald N. and DeYoreo, James J.},
  Journal                  = {J Am Chem Soc},
  Year                     = {2011},
  Number                   = {14},
  Pages                    = {5214--5217},
  Volume                   = {133}
}

@Article{Chen2016,
  Title                    = {Surface-Directed Assembly of Sequence-Defined Synthetic Polymers into Networks of Hexagonally-Patterned Nanoribbons with Controllable Functionalities},
  Author                   = {Chen, Chun-Long and Zuckermann, Ronald N and De Yoreo, James J},
  Journal                  = {ACS Nano},
  Year                     = {2016},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2016.05.08}
}

@Article{Chen2012,
  Title                    = {Towards the physical basis of how intrinsic disorder mediates protein function},
  Author                   = {Chen, Jianhan},
  Journal                  = {Archives of biochemistry and biophysics},
  Year                     = {2012},
  Number                   = {2},
  Pages                    = {123--131},
  Volume                   = {524},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.21}
}

@Article{Chen2007,
  Title                    = {A precise packing sequence for self-assembled convex structures},
  Author                   = {Chen, T. and Zhang, Z. and Glotzer, S. C.},
  Journal                  = PNAS,
  Year                     = {2007},
  Number                   = {3},
  Pages                    = {717--722},
  Volume                   = {104},

  File                     = {Chen2007.pdf:pdfs/Chen2007.pdf:PDF}
}

@Article{Chen2011,
  Title                    = {Expanded polyglutamine-binding peptoid as a novel therapeutic agent for treatment of Huntington's disease.},
  Author                   = {Chen, Xuesong and Wu, Jun and Luo, Yuan and Liang, Xia and Supnet, Charlene and Kim, Mee Whi and Lotz, Gregor P. and Yang, Guocheng and Muchowski, Paul J. and Kodadek, Thomas and Bezprozvanny, Ilya},
  Journal                  = {Chem Biol},
  Year                     = {2011},
  Number                   = {9},
  Pages                    = {1113--1125},
  Volume                   = {18}
}

@Article{Cheng2012,
  Title                    = {The odd–even effect of $^{20}$Ne fragmentation cross sections},
  Author                   = {J X Cheng and X Jiang and S W Yan, and D H Zhang},
  Journal                  = {J. Phys. G: Nucl. Part. Phys.},
  Year                     = {2012},
  Pages                    = {055104},
  Volume                   = {39},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Cheng2006,
  Title                    = {Rational drug design via intrinsically disordered protein},
  Author                   = {Cheng, Yugong and LeGall, Tanguy and Oldfield, Christopher J and Mueller, James P and Van, Ya-Yue J and Romero, Pedro and Cortese, Marc S and Uversky, Vladimir N and Dunker, A Keith},
  Journal                  = {Trends in biotechnology},
  Year                     = {2006},
  Number                   = {10},
  Pages                    = {435--442},
  Volume                   = {24},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.21}
}

@Article{Chervitz1998,
  Title                    = {Comparison of the complete protein sets of worm and yeast: orthology and divergence.},
  Author                   = {S. A. Chervitz and L. Aravind and G. Sherlock and C. A. Ball and E. V. Koonin and S. S. Dwight and M. A. Harris and K. Dolinski and S. Mohr and T. Smith and S. Weng and J. M. Cherry and D. Botstein},
  Journal                  = {Science},
  Year                     = {1998},

  Month                    = {Dec},
  Number                   = {5396},
  Pages                    = {2022--2028},
  Volume                   = {282},

  Abstract                 = {Comparative analysis of predicted protein sequences encoded by the genomes of Caenorhabditis elegans and Saccharomyces cerevisiae suggests that most of the core biological functions are carried out by orthologous proteins (proteins of different species that can be traced back to a common ancestor) that occur in comparable numbers. The specialized processes of signal transduction and regulatory control that are unique to the multicellular worm appear to use novel proteins, many of which re-use conserved domains. Major expansion of the number of some of these domains seen in the worm may have contributed to the advent of multicellularity. The proteins conserved in yeast and worm are likely to have orthologs throughout eukaryotes; in contrast, the proteins unique to the worm may well define metazoans.},
  File                     = {Chervitz1998.pdf:pdfs/Chervitz1998.pdf:PDF},
  Institution              = {, USA.},
  Keywords                 = {Animals; Caenorhabditis elegans, chemistry/genetics/physiology; Evolution, Molecular; Fungal Proteins, chemistry/genetics/physiology; Gene Expression Regulation; Genes, Fungal; Genes, Helminth; Helminth Proteins, chemistry/genetics/physiology; Saccharomyces cerevisiae, chemistry/genetics/physiology; Sequence Homology, Amino Acid; Signal Transduction},
  Owner                    = {ranjan},
  Pmid                     = {9851918},
  Timestamp                = {2011.03.03}
}

@Article{Chiti2009,
  Title                    = {Amyloid formation by globular proteins under native conditions.},
  Author                   = {Fabrizio Chiti and Christopher M Dobson},
  Journal                  = {Nat Chem Biol},
  Year                     = {2009},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {15--22},
  Volume                   = {5},

  Abstract                 = {The conversion of proteins from their soluble states into well-organized fibrillar aggregates is associated with a wide range of pathological conditions, including neurodegenerative diseases and systemic amyloidoses. In this review, we discuss the mechanism of aggregation of globular proteins under conditions in which they are initially folded. Although a conformational change of the native state is generally necessary to initiate aggregation, we show that a transition across the major energy barrier for unfolding is not essential and that aggregation may well be initiated from locally unfolded states that become accessible, for example, via thermal fluctuations occurring under physiological conditions. We review recent evidence on this topic and discuss its significance for understanding the onset and potential inhibition of protein aggregation in the context of diseases.},
  Institution              = {Dipartimento di Scienze Biochimiche, Universit? degli Studi di Firenze, Viale Morgagni 50, I-50134 Firenze, Italy. fabrizio.chiti@unifi.it},
  Keywords                 = {Amyloid, chemistry/metabolism; Humans; Models, Molecular; Protein Conformation; Protein Folding},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nchembio.131},
  Pmid                     = {19088715},
  Timestamp                = {2011.08.12}
}

@Article{Chiti2006,
  Title                    = {Protein misfolding, functional amyloid, and human disease.},
  Author                   = {Fabrizio Chiti and Christopher M Dobson},
  Journal                  = {Annu Rev Biochem},
  Year                     = {2006},
  Pages                    = {333--366},
  Volume                   = {75},

  Abstract                 = {Peptides or proteins convert under some conditions from their soluble forms into highly ordered fibrillar aggregates. Such transitions can give rise to pathological conditions ranging from neurodegenerative disorders to systemic amyloidoses. In this review, we identify the diseases known to be associated with formation of fibrillar aggregates and the specific peptides and proteins involved in each case. We describe, in addition, that living organisms can take advantage of the inherent ability of proteins to form such structures to generate novel and diverse biological functions. We review recent advances toward the elucidation of the structures of amyloid fibrils and the mechanisms of their formation at a molecular level. Finally, we discuss the relative importance of the common main-chain and side-chain interactions in determining the propensities of proteins to aggregate and describe some of the evidence that the oligomeric fibril precursors are the primary origins of 
pathological behavior.},
  Institution              = {Dipartimento di Scienze Biochimiche, Universit? degli Studi di Firenze, I-50134 Firenze, Italy. fabrizio.chiti@unifi.it},
  Keywords                 = {Amino Acid Sequence; Amyloid, chemistry/genetics/metabolism; Amyloidosis, metabolism/pathology/physiopathology; Humans; Models, Molecular; Neurodegenerative Diseases, metabolism/pathology/physiopathology; Polymorphism, Genetic; Protein Conformation; Protein Folding},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {16756495},
  Timestamp                = {2011.08.14}
}

@Article{Choe2000,
  Title                    = {Differential stabilization of two hydrophobic cores in the transition state of the villin 14T folding reaction.},
  Author                   = {S. E. Choe and L. Li and P. T. Matsudaira and G. Wagner and E. I. Shakhnovich},
  Journal                  = {J Mol Biol},
  Year                     = {2000},

  Month                    = {Nov},
  Number                   = {1},
  Pages                    = {99--115},
  Volume                   = {304},

  Abstract                 = {We report the distribution of hydrophobic core contacts during the folding reaction transition state for villin 14T, a small 126-residue protein domain. The solution structure of villin 14T contains a central beta-sheet with two flanking hydrophobic cores; transition states for this protein topology have not been previously studied. Villin 14T has no disulfide bonds or cis-proline residues in its native state; it folds reversibly, and in an apparently two-state manner under some conditions. To map the hydrophobic core contacts in the transition state, 27 point mutations were generated at positions spread throughout the two hydrophobic cores. After each point mutation, comparison of the change in folding kinetics with the equilibrium destabilization indicates whether the site of mutation is stabilized in the transition state. The results show that the folding nucleus, or the sub-region with the strongest transition state contacts, is located in one of the two hydrophobic cores (
the predominantly aliphatic core). The other hydrophobic core, which is mostly aromatic, makes much weaker contacts in the transition state. This work is the first transition state mapping for a protein with multiple major hydrophobic cores in a single folding unit; the hydrophobic cores cannot be separated into individual folding subdomains. The stabilization of only one hydrophobic core in the transition state illustrates that hydrophobic core formation is not intrinsically capable of nucleating folding, but must also involve the right specific interactions or topological factors in order to be kinetically important.},
  Institution              = {Department of Chemistry, Harvard University, Cambridge, MA 02138, USA.},
  Keywords                 = {Amino Acid Sequence; Amino Acid Substitution, genetics; Animals; Binding Sites; Carrier Proteins, chemistry/genetics/metabolism; Chickens; Conserved Sequence; Evolution, Molecular; Fluorescence; Kinetics; Microfilament Proteins, chemistry/genetics/metabolism; Models, Molecular; Molecular Sequence Data; Peptide Fragments, chemistry/genetics/metabolism; Point Mutation, genetics; Protein Denaturation, drug effects; Protein Folding; Protein Renaturation; Protein Structure, Secondary, drug effects; Protein Structure, Tertiary, drug effects; Thermodynamics; Tryptophan; Urea, pharmacology; Water, pharmacology},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(00)94190-1},
  Pmid                     = {11071813},
  Timestamp                = {2009.12.05}
}

@Article{Choi2006,
  Title                    = {Determinants of Bacteriophage $\phi$29 Head Morphology.},
  Author                   = {Choi, K.H. and Morais, M.C. and Anderson, D.L. and Rossmann, M.G.},
  Journal                  = {Structure},
  Year                     = {2006},
  Number                   = {11},
  Pages                    = {1723--1727},
  Volume                   = {14},

  File                     = {Choi2006.pdf:pdfs/Choi2006.pdf:PDF}
}

@Article{Chong2013,
  Title                    = {Conformational entropy of intrinsically disordered protein},
  Author                   = {Chong, Song-Ho and Ham, Sihyun},
  Journal                  = {The Journal of Physical Chemistry B},
  Year                     = {2013},
  Number                   = {18},
  Pages                    = {5503--5509},
  Volume                   = {117},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2015.09.17}
}

@Article{Chongsiriwatana2008,
  Title                    = {Peptoids that mimic the structure, function, and mechanism of helical antimicrobial peptides.},
  Author                   = {Chongsiriwatana, Nathaniel P. and Patch, James A. and Czyzewski, Ann M. and Dohm, Michelle T. and Ivankin, Andrey and Gidalevitz, David and Zuckermann, Ronald N. and Barron, Annelise E.},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2008},

  Month                    = {Feb},
  Number                   = {8},
  Pages                    = {2794--2799},
  Volume                   = {105},

  Abstract                 = {Antimicrobial peptides (AMPs) and their mimics are emerging as promising antibiotic agents. We present a library of ``ampetoids'' (antimicrobial peptoid oligomers) with helical structures and biomimetic sequences, several members of which have low-micromolar antimicrobial activities, similar to cationic AMPs like pexiganan. Broad-spectrum activity against six clinically relevant BSL2 pathogens is also shown. This comprehensive structure-activity relationship study, including circular dichroism spectroscopy, minimum inhibitory concentration assays, hemolysis and mammalian cell toxicity studies, and specular x-ray reflectivity measurements shows that the in vitro activities of ampetoids are strikingly similar to those of AMPs themselves, suggesting a strong mechanistic analogy. The ampetoids' antibacterial activity, coupled with their low cytotoxicity against mammalian cells, make them a promising class of antimicrobials for biomedical applications. Peptoids are biostable, with a 
protease-resistant N-substituted glycine backbone, and their sequences are highly tunable, because an extensive diversity of side chains can be incorporated via facile solid-phase synthesis. Our findings add to the growing evidence that nonnatural foldamers will emerge as an important class of therapeutics.},
  Institution              = {Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {0708254105},
  Pmid                     = {18287037},
  Timestamp                = {2012.07.15}
}

@Article{Chothia2003,
  Title                    = {Evolution of the Protein Repertoire},
  Author                   = {Chothia,C. and Gough,J. and Vogel,C. and Teichmann,S.A.},
  Journal                  = {Science},
  Year                     = {2003},
  Pages                    = {1701--1703},
  Volume                   = {300},

  File                     = {Chothia2003.pdf:pdfs/Chothia2003.pdf:PDF},
  Owner                    = {ranjan},
  Timestamp                = {2009.08.21}
}

@Article{Chothia1997,
  Title                    = {Protein folds in the all-beta and all-alpha classes.},
  Author                   = {C. Chothia and T. Hubbard and S. Brenner and H. Barns and A. Murzin},
  Journal                  = {Annu Rev Biophys Biomol Struct},
  Year                     = {1997},
  Pages                    = {597--627},
  Volume                   = {26},

  Abstract                 = {Analysis of the structures in the Protein Databank, released in June 1996, shows that the number of different protein folds, i.e. the number of different arrangements of major secondary structures and/or chain topologies, is 327. Of these folds, approximately 25\% belong to the all-alpha class, 20\% belong to the all-beta class, 30\% belong to the alpha/beta class, and 25\% belong to the alpha + beta class. We describe the types of folds now known for the all-beta and all-alpha classes, emphasizing those that have been discovered recently. Detailed theories for the physical determinants of the structures of most of these folds now exist, and these are reviewed.},
  File                     = {Chothia1997.pdf:pdfs/Chothia1997.pdf:PDF},
  Institution              = {MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.},
  Keywords                 = {Databases, Factual; Protein Folding; Protein Structure, Secondary; Proteins, chemistry},
  Owner                    = {ranjan},
  Pmid                     = {9241431},
  Timestamp                = {2009.09.11}
}

@Article{Cintas2002,
  Title                    = {Chirality of living systems: a helping hand from crystals and oligopeptides},
  Author                   = {Cintas, Pedro},
  Journal                  = {Angewandte Chemie International Edition},
  Year                     = {2002},
  Number                   = {7},
  Pages                    = {1139--1145},
  Volume                   = {41},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2016.06.06}
}

@Article{Clark2006,
  Title                    = {Trends in antibody sequence changes during the somatic hypermutation process.},
  Author                   = {Louis A Clark and Skanth Ganesan and Sarah Papp and Herman W T van Vlijmen},
  Journal                  = {J Immunol},
  Year                     = {2006},

  Month                    = {Jul},
  Number                   = {1},
  Pages                    = {333--340},
  Volume                   = {177},

  Abstract                 = {Probable germline gene sequences from thousands of aligned mature Ab sequences are inferred using simple computational matching to known V(D)J genes. Comparison of the germline to mature sequences in a structural region-dependent fashion allows insights into the methods that nature uses to mature Abs during the somatic hypermutation process. Four factors determine the residue type mutation patterns: biases in the germline, accessibility from single base permutations, location of mutation hotspots, and functional pressures during selection. Germline repertoires at positions that commonly contact the Ag are biased with tyrosine, serine, and tryptophan. These residue types have a high tendency to be present in mutation hotspot motifs, and their abundance is decreased during maturation by a net conversion to other types. The heavy use of tyrosines on mature Ab interfaces is thus a reflection of the germline composition rather than being due to selection during maturation. 
Potentially stabilizing changes such as increased proline usage and a small number of double cysteine mutations capable of forming disulfide bonds are ascribed to somatic hypermutation. Histidine is the only residue type for which usage increases in each of the interface, core, and surface regions. The net overall effect is a conversion from residue types that could provide nonspecific initial binding into a diversity of types that improve affinity and stability. Average mutation probabilities are approximately 4\% for core residues, approximately 5\% for surface residues, and approximately 12\% for residues in common Ag-contacting positions, excepting the those coded by the D gene.},
  File                     = {Clark2006.pdf:pdfs/Clark2006.pdf:PDF},
  Institution              = {Biogen Idec Inc., 14 Cambridge Center, Cambridge, MA 02142, USA. louie@alumni.northwestern.edu},
  Keywords                 = {Amino Acid Sequence, genetics; Amino Acid Substitution, genetics/immunology; Binding Sites, Antibody, genetics; Gene Rearrangement, B-Lymphocyte, Heavy Chain; Gene Rearrangement, B-Lymphocyte, Light Chain; Germ-Line Mutation; Immunoglobulin Heavy Chains, chemistry/genetics/metabolism; Immunoglobulin Light Chains, chemistry/genetics/metabolism; Immunoglobulin Variable Region, chemistry/genetics/metabolism; Molecular Sequence Data; Probability; Protein Structure, Tertiary, genetics; Serine, genetics; Somatic Hypermutation, Immunoglobulin; Tryptophan, genetics; Tyrosine, genetics},
  Owner                    = {ranjan},
  Pii                      = {177/1/333},
  Pmid                     = {16785529},
  Timestamp                = {2010.01.01}
}

@Article{Clouet2006,
  Title                    = {Complex precipitation pathways in multicomponent alloys},
  Author                   = {Clouet, Emmanuel and La{\'e}, Ludovic and {\'E}picier, Thierry and Lefebvre, Williams and Nastar, Maylise and Deschamps, Alexis},
  Journal                  = {Nature materials},
  Year                     = {2006},
  Number                   = {6},
  Pages                    = {482--488},
  Volume                   = {5},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2015.04.20}
}

@Article{Cock2009,
  Title                    = {Biopython: freely available Python tools for computational molecular biology and bioinformatics.},
  Author                   = {Cock,P.J. and Antao,T. and Chang,J.T. and Chapman,B.A. and Cox,C.J. and Dalke,A. and Friedberg,I. and Hamelryck,T. and Kauff,F. and Wilczynski,B. and de Hoon,M.J.},
  Journal                  = {Bioinformatics},
  Year                     = {2009},
  Number                   = {11},
  Pages                    = {1422--1423},
  Volume                   = {25}
}

@Article{Cole2002,
  Title                    = {Side-chain conformational entropy at protein-protein interfaces.},
  Author                   = {Christian Cole and Jim Warwicker},
  Journal                  = {Protein Sci},
  Year                     = {2002},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {2860--2870},
  Volume                   = {11},

  Abstract                 = {Protein-protein interactions are the key to many biological processes. How proteins selectively and correctly associate with their required protein partner(s) is still unclear. Previous studies of this "protein-docking problem" have found that shape complementarity is a major determinant of interaction, but the detailed balance of energy contributions to association remains unclear. This study estimates side-chain conformational entropy (per unit solvent accessible area) for various protein surface regions, using a self-consistent mean field calculation of rotamer probabilities. Interfacial surface regions were less flexible than the rest of the protein surface for calculations with monomers extracted from homodimer datasets in 21 of 25 cases, and in 8 of 9 for the large protomer from heterodimer datasets. In surface patch analysis, based on side-chain conformational entropy, 68\% of true interfaces were ranked top for the homodimer set and 66\% for the large protomer/
heterodimer set. The results indicate that addition of a side-chain entropic term could significantly improve empirical calculations of protein-protein association.},
  Institution              = {Department of Biomolecular Sciences, UMIST, Manchester M60 1QD, UK.},
  Keywords                 = {Binding Sites; Entropy; Models, Molecular; Pliability; Protein Binding; Protein Conformation; Protein Interaction Mapping; Proteins, chemistry/metabolism},
  Owner                    = {ranjan},
  Pmid                     = {12441384},
  Timestamp                = {2010.02.14}
}

@Article{Conant2008,
  Title                    = {Turning a hobby into a job: how duplicated genes find new functions.},
  Author                   = {Gavin C Conant and Kenneth H Wolfe},
  Journal                  = {Nat Rev Genet},
  Year                     = {2008},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {938--950},
  Volume                   = {9},

  Abstract                 = {Gene duplication provides raw material for functional innovation. Recent advances have shed light on two fundamental questions regarding gene duplication: which genes tend to undergo duplication? And how does natural selection subsequently act on them? Genomic data suggest that different gene classes tend to be retained after single-gene and whole-genome duplications. We also know that functional differences between duplicate genes can originate in several different ways, including mutations that directly impart new functions, subdivision of ancestral functions and selection for changes in gene dosage. Interestingly, in many cases the 'new' function of one copy is a secondary property that was always present, but that has been co-opted to a primary role after the duplication.},
  Institution              = {Division of Animal Sciences, University of Missouri-Columbia, 163B Animal Sciences Center, 920 East Campus Drive, Columbia, Missouri 65211-5300, USA.},
  Keywords                 = {Animals; Galactokinase, genetics; Gene Dosage; Gene Duplication; Gene Expression; Genome; Humans; Mutation; Saccharomyces cerevisiae Proteins, genetics; Saccharomyces cerevisiae, genetics; Selection, Genetic; Transcription Factors, genetics},
  Owner                    = {ranjan},
  Pii                      = {nrg2482},
  Pmid                     = {19015656},
  Timestamp                = {2010.04.20}
}

@Article{Conway2001,
  Title                    = {Virus maturation involving large subunit rotations and local refolding.},
  Author                   = {Conway,J.F. and Wikoff,W.R. and Cheng,N. and Duda,R.L. and Hendrix,R.W. and Johnson,J.E. and Steven,A.C.},
  Journal                  = {Science.},
  Year                     = {2001},
  Number                   = {5517},
  Pages                    = {744-748},
  Volume                   = {292},

  File                     = {Conway2001.pdf:pdfs/Conway2001.pdf:PDF}
}

@Article{Conway2007,
  Title                    = {A thermally induced phase transition in a viral capsid transforms the hexamers, leaving the pentamers unchanged},
  Author                   = {Conway, J. F. and Cheng, N. and Ross, P. D. and Hendrix, R. W. and Duda, R. L. and Steven, A. C.},
  Journal                  = {J. Struct. Biol.},
  Year                     = {2007},
  Number                   = {2},
  Pages                    = {224--232},
  Volume                   = {158},

  File                     = {Conway2007.pdf:pdfs/Conway2007.pdf:PDF}
}

@Book{Cooper2000,
  Title                    = {The Cell: A Molecular Approach},
  Author                   = {Cooper, Geoffrey M and Hausman, Robert E},
  Publisher                = {Sinauer Associates, Inc.},
  Year                     = {2013},

  Address                  = {Sunderland, MA},
  Edition                  = {6},

  Owner                    = {ranjan},
  Timestamp                = {2013.07.20}
}

@Article{Copley2003,
  Title                    = {Enzymes with extra talents: moonlighting functions and catalytic promiscuity.},
  Author                   = {Shelley D Copley},
  Journal                  = {Curr Opin Chem Biol},
  Year                     = {2003},

  Month                    = {Apr},
  Number                   = {2},
  Pages                    = {265--272},
  Volume                   = {7},

  Abstract                 = {Recent studies of moonlighting functions and catalytic promiscuity provide insights into the structural and mechanistic bases of these phenomena. Moonlighting proteins that are highlighted include gephyrin, the Neurospora crassa tyrosyl tRNA synthetase, phosphoglucose isomerase, and cytochrome c. New insights into catalytic promiscuity are provided by studies of aminoglycoside kinase (3') type IIIa, tetrachlorohydroquinone dehalogenase, and aldolase antibody 38C2.},
  File                     = {Copley2003.pdf:pdfs/Copley2003.pdf:PDF},
  Institution              = {Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder Campus, Box 216, Boulder, CO 80309-0216, USA. copley@cires.colorado.edu},
  Keywords                 = {Animals; Catalysis; Enzymes, metabolism; Humans; Substrate Specificity},
  Owner                    = {ranjan},
  Pii                      = {S1367593103000322},
  Pmid                     = {12714060},
  Timestamp                = {2011.03.09}
}

@Article{Coulibaly2005,
  Title                    = {The birnavirus crystal structure reveals structural relationships among icosahedral viruses.},
  Author                   = {Coulibaly, F. and Chevalier, C. and Gutsche, I. and Pous, J. and Navaza, J. and Bressanelli, S. and Delmas, B. and Rey, F. A.},
  Journal                  = {Cell (Cambridge, Mass., USA)},
  Year                     = {2005},
  Pages                    = {761},
  Volume                   = {120},

  File                     = {Coulibaly2005.pdf:pdfs/Coulibaly2005.pdf:PDF}
}

@Article{Cowley1975,
  Title                    = {Nuclear and nonnuclear abundance patterns in the manganese stars},
  Author                   = {Cowley, C. R. and Aikman, G. C. L.},
  Journal                  = {The Astrophysical Journal},
  Year                     = {1975},

  Month                    = {Mar},
  Pages                    = {521},
  Volume                   = {196},

  Doi                      = {10.1086/153432},
  Owner                    = {ranjan},
  Publisher                = {IOP Publishing},
  Timestamp                = {2014.01.17}
}

@Article{Cozzetto2013,
  Title                    = {The contribution of intrinsic disorder prediction to the elucidation of protein function},
  Author                   = {Cozzetto, Domenico and Jones, David T},
  Journal                  = {Current opinion in structural biology},
  Year                     = {2013},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.18}
}

@Book{Cramer2004,
  Title                    = {Essentials of Computational Chemistry: Theories and Models},
  Author                   = {Christopher J. Cramer},
  Publisher                = {Wiley},
  Year                     = {2004},
  Edition                  = {2},

  Owner                    = {ranjan},
  Timestamp                = {2012.07.14}
}

@Article{Crapster2013,
  Title                    = {A Peptoid Ribbon Secondary Structure},
  Author                   = {Crapster, J Aaron and Guzei, Ilia A and Blackwell, Helen E},
  Journal                  = {Angewandte Chemie International Edition},
  Year                     = {2013},
  Number                   = {19},
  Pages                    = {5079--5084},
  Volume                   = {52},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2014.07.23}
}

@Article{Crapster2011,
  Title                    = {Design and conformational analysis of peptoids containing N-hydroxy amides reveals a unique sheet-like secondary structure.},
  Author                   = {Crapster, J Aaron and Stringer, Joseph R. and Guzei, Ilia A. and Blackwell, Helen E.},
  Journal                  = {Biopolymers},
  Year                     = {2011},
  Number                   = {5},
  Pages                    = {604--616},
  Volume                   = {96},

  Abstract                 = {N-hydroxy amides can be found in many naturally occurring and synthetic compounds and are known to act as both strong proton donors and chelators of metal cations. We have initiated studies of peptoids, or N-substituted glycines which contain N-hydroxy amide side chains to investigate the potential effects of these functional groups on peptoid backbone amide rotamer equilibria and local conformations. We reasoned that the propensity of these functional groups to participate in hydrogen bonding could be exploited to enforce intramolecular or intermolecular interactions that yield new peptoid structures. Here, we report the design, synthesis, and detailed conformational analysis of a series of model N-hydroxy peptoids. These peptoids were readily synthesized, and their structures were analyzed in solution by 1D and 2D NMR and in the solid-state by X-ray crystallography. The N-hydroxy amides were found to strongly favor trans conformations with respect to the peptoid backbone in 
chloroform. More notably, unique sheet-like structures held together via intermolecular hydrogen bonds were observed in the X-ray crystal structures of an N-hydroxy amide peptoid dimer, which to our knowledge represent the first structure of this type reported for peptoids. These results suggest that the N-hydroxy amide can be utilized to control both local backbone geometries and longer-range intermolecular interactions in peptoids, and represents a new functional group in the peptoid design toolbox.},
  Institution              = {Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA.},
  Keywords                 = {Acylation; Amides, chemical synthesis/chemistry; Crystallography, X-Ray; Drug Design; Hydrogen Bonding; Magnetic Resonance Spectroscopy; Molecular Structure; Peptoids, chemical synthesis/chemistry; Protein Structure, Secondary},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {22180908},
  Timestamp                = {2012.06.19}
}

@Article{Crick1956,
  Title                    = {Structure of small viruses.},
  Author                   = {Crick,F.H. and Watson,J.D.},
  Journal                  = {Nature.},
  Year                     = {1956},
  Number                   = {4506},
  Pages                    = {473-475},
  Volume                   = {177},

  File                     = {Crick1956.pdf:pdfs/Crick1956.pdf:PDF}
}

@Article{Csermely2010,
  Title                    = {Induced fit, conformational selection and independent dynamic segments: an extended view of binding events},
  Author                   = {Csermely, Peter and Palotai, Robin and Nussinov, Ruth},
  Journal                  = {Trends in biochemical sciences},
  Year                     = {2010},
  Number                   = {10},
  Pages                    = {539--546},
  Volume                   = {35},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.17}
}

@Article{Cui2002,
  Title                    = {Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes.},
  Author                   = {Yan Cui and Wing Hung Wong and Erich Bornberg-Bauer and Hue Sun Chan},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2002},

  Month                    = {Jan},
  Number                   = {2},
  Pages                    = {809--814},
  Volume                   = {99},

  Abstract                 = {The role of recombination in evolution is compared with that of point mutations (substitutions) in the context of a simple, polymer physics-based model mapping between sequence (genotype) and conformational (phenotype) spaces. Crossovers and point mutations of lattice chains with a hydrophobic polar code are investigated. Sequences encoding for a single ground-state conformation are considered viable and used as model proteins. Point mutations lead to diffusive walks on the evolutionary landscape, whereas crossovers can "tunnel" through barriers of diminished fitness. The degree to which crossovers allow for more efficient sequence and structural exploration depends on the relative rates of point mutations versus that of crossovers and the dispersion in fitness that characterizes the ruggedness of the evolutionary landscape. The probability that a crossover between a pair of viable sequences results in viable sequences is an order of magnitude higher than random, implying that a 
sequence's overall propensity to encode uniquely is embodied partially in local signals. Consistent with this observation, certain hydrophobicity patterns are significantly more favored than others among fragments (i.e., subsequences) of sequences that encode uniquely, and examples reminiscent of autonomous folding units in real proteins are found. The number of structures explored by both crossovers and point mutations is always substantially larger than that via point mutations alone, but the corresponding numbers of sequences explored can be comparable when the evolutionary landscape is rugged. Efficient structural exploration requires intermediate nonextreme ratios between point-mutation and crossover rates.},
  Institution              = {Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.},
  Keywords                 = {Biophysical Phenomena; Biophysics; Biopolymers, chemistry; Evolution, Molecular; Models, Genetic; Models, Molecular; Point Mutation; Protein Folding; Proteins, chemistry/genetics; Recombination, Genetic; Thermodynamics; Time Factors},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {99/2/809},
  Pmid                     = {11805332},
  Timestamp                = {2011.11.22}
}

@Article{Culf2010,
  Title                    = {Solid-Phase Synthesis of N-Substituted Glycine Oligomers ($\alpha$-Peptoids) and Derivatives},
  Author                   = {Culf, Adrian S and Ouellette, Rodney J},
  Journal                  = {Molecules},
  Year                     = {2010},
  Number                   = {8},
  Pages                    = {5282--5335},
  Volume                   = {15},

  Owner                    = {ranjan},
  Publisher                = {Molecular Diversity Preservation International},
  Timestamp                = {2014.06.11}
}

@Article{DAlessandro2004,
  Title                    = {Characterization of the conformational behavior of peptide Contryphan Vn: a theoretical study.},
  Author                   = {D'Alessandro, M. and Paci, M. and Amadei, A.},
  Journal                  = {Biopolymers},
  Year                     = {2004},

  Month                    = {Aug},
  Number                   = {6},
  Pages                    = {448--456},
  Volume                   = {74},

  Abstract                 = {In this work we report the study of a peptide, the Contryphan Vn produced by Conus ventricosus, a vermivorous cone snail living in the temperate Mediterranean sea. This cyclic peptide of nine residues is a ring closed by a Cys-Cys (Cys: cysteine) disulfide bond containing two proline (Pro) residues and two tryptophans (Trp), one of them being a D-Trp. We present a statistical mechanical characterization of the peptide, simulated in water for about 200 ns with classical molecular dynamics (MD). In recent years there has been a growing interest in the study of the mechanics and dynamics of biological molecules, and in particular for proteins and peptides, about the relationship between collective motions and the active conformations which exert the biological function. To this aim we used the essential dynamics analysis on the MD trajectory and extracted, from the total fluctuations of the molecule, the dominant dynamical modes responsible of the principal conformational 
transitions. The Contryphan Vn small size allowed us to investigate in details the all-atoms dynamics and the corresponding thermodynamics in conformational space defined by the most significant intramolecular motions.},
  Doi                      = {10.1002/bip.20090},
  Institution              = {Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, via della Ricerca Scientifica 1, 00133 Roma, Italy.},
  Keywords                 = {Animals; Computer Simulation; Disulfides; Models, Molecular; Models, Statistical; Peptides, Cyclic, chemistry; Peptides, chemistry; Proline, chemistry; Protein Conformation; Snails; Temperature; Thermodynamics; Time Factors; Tryptophan, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {15274088},
  Timestamp                = {2014.02.07}
}

@Article{DOnofrio1999,
  Title                    = {The correlation of protein hydropathy with the base composition of coding sequences.},
  Author                   = {D'Onofrio, G. and Jabbari, K. and Musto, H. and Bernardi, G.},
  Journal                  = {Gene},
  Year                     = {1999},

  Month                    = {Sep},
  Number                   = {1},
  Pages                    = {3--14},
  Volume                   = {238},

  Abstract                 = {The "universal correlation" (D'Onofrio, G., Bernardi, G., 1992. A universal compositional correlation among codon positions. Gene 110, 81-88.) that holds between <GC3> and <GC1> or <GC2> (<GC> values are the average values of the coding sequences of each genome analyzed) at both the inter- and intra-genomic level, was re-analyzed on a vastly larger dataset. The results showed a slight, but significant, difference in the <GC3> vs. <GC1> correlations exhibited by prokaryotes and eukaryotes. This finding prompted an analysis of the correlation between <GC3> and the amino acid frequencies in the encoded proteins, which has shown that positive correlations exist between <GC3> values of coding sequences and the hydropathy of the corresponding proteins. These correlations are due to the fact that hydrophobic and amphypathic amino acids increase, whereas hydrophilic amino acids decrease with increasing <GC3> values. Hydropathy values of prokaryotic proteins are systematically higher 
than those of eukaryotes, but the slopes of the regression lines are identical. The lower hydrophobicity of eukaryotic proteins is due to differences in the amino acid composition. In particular, the twofold higher cysteine (and disulfide bond) level of eukaryotic proteins compared to prokaryotic proteins most probably compensates for their lower hydrophobicity. This supports the viewpoint that hydrophobicity plays a structural and functional role as far as protein stability is concerned.},
  Institution              = {Laboratorio di Evoluzione Molecolare, Stazione Zoologica Anton Dohrn, Napoli, Italy.},
  Keywords                 = {Amino Acids, chemistry; Base Composition; Base Sequence; Codon; Genome; Proteins, chemistry/genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0378-1119(99)00257-7},
  Pmid                     = {10570978},
  Timestamp                = {2012.09.27}
}

@Article{Daggett2006,
  Title                    = {$\alpha$-Sheet: the toxic conformer in amyloid diseases?},
  Author                   = {Daggett, Valerie},
  Journal                  = {Accounts of chemical research},
  Year                     = {2006},
  Number                   = {9},
  Pages                    = {594--602},
  Volume                   = {39},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2015.11.15}
}

@Article{Dandekar1998,
  Title                    = {Conservation of gene order: a fingerprint of proteins that physically interact.},
  Author                   = {T. Dandekar and B. Snel and M. Huynen and P. Bork},
  Journal                  = {Trends Biochem Sci},
  Year                     = {1998},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {324--328},
  Volume                   = {23},

  Abstract                 = {A systematic comparison of nine bacterial and archaeal genomes reveals a low level of gene-order (and operon architecture) conservation. Nevertheless, a number of gene pairs are conserved. The proteins encoded by conserved gene pairs appear to interact physically. This observation can therefore be used to predict functions of, and interactions between, prokaryotic gene products.},
  Institution              = {European Molecular Biology Laboratory, Heidelberg, Germany.},
  Keywords                 = {Archaeal Proteins, chemistry/genetics; Bacterial Proteins, chemistry/genetics; Evolution, Molecular; Genes, Archaeal; Genes, Bacterial; Multigene Family; Operon; Protein Folding},
  Owner                    = {ranjan},
  Pii                      = {S0968-0004(98)01274-2},
  Pmid                     = {9787636},
  Timestamp                = {2010.05.20}
}

@Article{pme,
  Title                    = {{Particle Mesh Ewald: an N*LOG(N) method for Ewald sums in large systems}},
  Author                   = {T. Darden and D. York and L. Pederson},
  Journal                  = {J. Chem. Phys.},
  Year                     = {1993},
  Pages                    = {10089},
  Volume                   = {98}
}

@Book{Darwin1859,
  Title                    = {On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life},
  Author                   = {Charles Darwin},
  Publisher                = {London: John Murray},
  Year                     = {1859},
  Edition                  = {1},

  Owner                    = {ranjan},
  Timestamp                = {2009.11.28}
}

@Article{Das2001,
  Title                    = {X-ray crystal structure of MTH938 from Methanobacterium thermoautotrophicum at 2.2 A resolution reveals a novel tertiary protein fold.},
  Author                   = {K. Das and R. Xiao and E. Wahlberg and F. Hsu and C. H. Arrowsmith and G. T. Montelione and E. Arnold},
  Journal                  = {Proteins},
  Year                     = {2001},

  Month                    = {Dec},
  Number                   = {4},
  Pages                    = {486--488},
  Volume                   = {45},

  Institution              = {Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, USA.},
  Keywords                 = {Amino Acid Sequence; Bacterial Proteins, chemistry; Crystallography, X-Ray; Humans; Methanobacterium, chemistry; Models, Molecular; Molecular Sequence Data; Protein Structure, Secondary; Protein Structure, Tertiary; Sequence Alignment; Sequence Homology, Amino Acid},
  Owner                    = {ranjan},
  Pii                      = {10.1002/prot.1162},
  Pmid                     = {11746696},
  Timestamp                = {2010.09.20}
}

@Article{Das2013,
  Title                    = {Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues},
  Author                   = {Das, Rahul K and Pappu, Rohit V},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2013},
  Number                   = {33},
  Pages                    = {13392--13397},
  Volume                   = {110},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2015.09.17}
}

@Article{Davies2008,
  Title                    = {Optimizing amino acid groupings for GPCR classification.},
  Author                   = {Matthew N Davies and Andrew Secker and Alex A Freitas and Edward Clark and Jon Timmis and Darren R Flower},
  Journal                  = {Bioinformatics},
  Year                     = {2008},

  Month                    = {Sep},
  Number                   = {18},
  Pages                    = {1980--1986},
  Volume                   = {24},

  Abstract                 = {MOTIVATION: There is much interest in reducing the complexity inherent in the representation of the 20 standard amino acids within bioinformatics algorithms by developing a so-called reduced alphabet. Although there is no universally applicable residue grouping, there are numerous physiochemical criteria upon which one can base groupings. Local descriptors are a form of alignment-free analysis, the efficiency of which is dependent upon the correct selection of amino acid groupings. RESULTS: Within the context of G-protein coupled receptor (GPCR) classification, an optimization algorithm was developed, which was able to identify the most efficient grouping when used to generate local descriptors. The algorithm was inspired by the relatively new computational intelligence paradigm of artificial immune systems. A number of amino acid groupings produced by this algorithm were evaluated with respect to their ability to generate local descriptors capable of providing an accurate 
classification algorithm for GPCRs.},
  File                     = {Davies2008.pdf:pdfs/Davies2008.pdf:PDF},
  Institution              = {Edward Jenner Institute, Compton, Newbury, Berkshire, UK.},
  Keywords                 = {Algorithms; Amino Acids, classification; Artificial Intelligence; Computational Biology, methods; Databases, Protein; Receptors, G-Protein-Coupled, chemistry/classification/metabolism; Sequence Analysis, Protein, methods},
  Owner                    = {ranjan},
  Pii                      = {btn382},
  Pmid                     = {18676973},
  Timestamp                = {2009.10.03}
}

@Article{Dean2007,
  Title                    = {Mechanistic approaches to the study of evolution: the functional synthesis.},
  Author                   = {Antony M Dean and Joseph W Thornton},
  Journal                  = {Nat Rev Genet},
  Year                     = {2007},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {675--688},
  Volume                   = {8},

  Abstract                 = {An emerging synthesis of evolutionary biology and experimental molecular biology is providing much stronger and deeper inferences about the dynamics and mechanisms of evolution than were possible in the past. The new approach combines statistical analyses of gene sequences with manipulative molecular experiments to reveal how ancient mutations altered biochemical processes and produced novel phenotypes. This functional synthesis has set the stage for major advances in our understanding of fundamental questions in evolutionary biology. Here we describe this emerging approach, highlight important new insights that it has made possible, and suggest future directions for the field.},
  Institution              = {University of Minnesota, St Paul, Minnesota 55108, USA. deanx024@umn.edu},
  Keywords                 = {Adaptation, Biological; Animals; Color Perception, genetics; Directed Molecular Evolution, methods; Drug Resistance, genetics; Evolution; Humans; Insecticide Resistance, genetics; Mice; Models, Biological; Molecular Biology, methods; Phylogeny; Pigmentation, genetics; Protein Engineering, methods; Proteins, genetics/physiology; Selection, Genetic},
  Owner                    = {ranjan},
  Pii                      = {nrg2160},
  Pmid                     = {17703238},
  Timestamp                = {2010.04.20}
}

@Article{Deeds2003,
  Title                    = {Protein evolution within a structural space.},
  Author                   = {Eric J Deeds and Nikolay V Dokholyan and Eugene I Shakhnovich},
  Journal                  = {Biophys J},
  Year                     = {2003},

  Month                    = {Nov},
  Number                   = {5},
  Pages                    = {2962--2972},
  Volume                   = {85},

  Abstract                 = {Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might impact protein structural evolution. We approach this question using lattice polymers as a completely characterized model of this space. We develop a measure of structural comparison of lattice structures that is analogous to the one used to understand structural similarities between real proteins. We use this measure of structural relatedness to create a graph of lattice structures and compare this graph (in which nodes are lattice structures and edges are defined using structural similarity) to the graph obtained for real protein structures. We find that the graph obtained from all compact lattice structures exhibits a distribution of structural neighbors per node consistent with a random graph. We also find that subgraphs of 3500 nodes 
chosen either at random or according to physical constraints also represent random graphs. We develop a divergent evolution model based on the lattice space which produces graphs that, within certain parameter regimes, recapitulate the scale-free behavior observed in similar graphs of real protein structures.},
  File                     = {Deeds2003.pdf:pdfs/Deeds2003.pdf:PDF},
  Institution              = {Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.},
  Keywords                 = {Amino Acid Sequence; Computer Simulation; Evolution, Molecular; Models, Chemical; Models, Genetic; Models, Molecular; Models, Statistical; Molecular Sequence Data; Proteins, chemistry/genetics; Sequence Homology, Amino Acid},
  Owner                    = {ranjan},
  Pii                      = {S0006-3495(03)74716-X},
  Pmid                     = {14581198},
  Timestamp                = {2009.12.05}
}

@Article{Deeds2005a,
  Title                    = {Prokaryotic phylogenies inferred from protein structural domains.},
  Author                   = {Eric J Deeds and Hooman Hennessey and Eugene I Shakhnovich},
  Journal                  = {Genome Res},
  Year                     = {2005},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {393--402},
  Volume                   = {15},

  Abstract                 = {The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this work, we explore a new source of phylogenetic information, the distribution of protein structural domains within fully sequenced prokaryotic genomes. The evolution of the structural domains we use has been studied extensively, allowing us to base our phylogenetic methods on testable theoretical models of structural evolution. We find that the methods that produce reasonable phylogenetic relationships are indeed the methods that are most consistent with theoretical evolutionary models. This work represents, to our knowledge, the first such theoretically motivated phylogeny, as well as the first application of structural information to phylogeny on this scale. Our 
results have strong implications for the phylogenetic relationships among prokaryotic organisms and for the understanding of protein evolution as a whole.},
  Institution              = {Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.},
  Keywords                 = {Archaeal Proteins, chemistry/genetics; Bacterial Proteins, chemistry/genetics; Evolution, Molecular; Fungal Proteins, chemistry/genetics; Gene Transfer, Horizontal; Genomics; Models, Genetic; Phylogeny; Prokaryotic Cells; Protein Structure, Tertiary; Proteins, chemistry/genetics; Proteome},
  Owner                    = {ranjan},
  Pii                      = {15/3/393},
  Pmid                     = {15741510},
  Timestamp                = {2009.12.05}
}

@Article{Deeds2004,
  Title                    = {Proteomic traces of speciation.},
  Author                   = {Eric J Deeds and Boris Shakhnovich and Eugene I Shakhnovich},
  Journal                  = {J Mol Biol},
  Year                     = {2004},

  Month                    = {Feb},
  Number                   = {3},
  Pages                    = {695--706},
  Volume                   = {336},

  Abstract                 = {Recent work has shown that the network of structural similarity between protein domains exhibits a power-law distribution of edges per node. The scale-free nature of this graph, termed the protein domain universe graph or PDUG, may be reproduced via a divergent model of structural evolution. The performance of this model, however, does not preclude the existence of a successful convergent model. To further resolve the issue of protein structural evolution, we explore the predictions of both convergent and divergent models directly. We show that when nodes from the PDUG are partitioned into subgraphs on the basis of their occurrence in the proteomes of particular organisms, these subgraphs exhibit a scale-free nature as well. We explore a simple convergent model of structural evolution and find that the implications of this model are inconsistent with features of these organismal subgraphs. Importantly, we find that biased convergent models are inconsistent with our data. We find 
that when speciation mechanisms are added to a simple divergent model, subgraphs similar to the organismal subgraphs are produced, demonstrating that dynamic models can easily explain the distributions of structural similarity that exist within proteomes. We show that speciation events must be included in a divergent model of structural evolution to account for the non-random overlap of structural proteomes. These findings have implications for the long-standing debate over convergent and divergent models of protein structural evolution, and for the study of the evolution of organisms as a whole.},
  File                     = {Deeds2004.pdf:pdfs/Deeds2004.pdf:PDF},
  Institution              = {Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue Cambridge, MA 02138, USA.},
  Keywords                 = {Bacterial Proteins, chemistry/genetics; Evolution; Models, Theoretical; Protein Conformation; Protein Structure, Tertiary; Proteome},
  Owner                    = {ranjan},
  Pii                      = {S0022283604000166},
  Pmid                     = {15095981},
  Timestamp                = {2009.12.05}
}

@Article{Deeds2007,
  Title                    = {A structure-centric view of protein evolution, design, and adaptation.},
  Author                   = {Eric J Deeds and Eugene I Shakhnovich},
  Journal                  = {Adv Enzymol Relat Areas Mol Biol},
  Year                     = {2007},
  Pages                    = {133--91, xi-xii},
  Volume                   = {75},

  Abstract                 = {Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent in the indispensability of proteins for living cells is the fact that a given protein can adopt a specific three-dimensional shape that is specified solely by the protein's sequence of amino acids. Over the past several decades, structural biologists have demonstrated that the array of structures that proteins may adopt is quite astounding, and this has lead to a strong interest in understanding how protein structures change and evolve over time. In this review we consider a large body of recent work that attempts to illuminate this structure-centric picture of protein evolution. Much of this work has focused on the question of how completely new protein structures (i.e., new folds or topologies) are discovered by protein sequences as they evolve. Pursuant to this question of structural innovation has been a desire to describe 
and understand the observation that certain types of protein structures are far more abundant than others and how this uneven distribution of proteins implicates on the process through which new shapes are discovered. We consider a number of theoretical models that have been successful at explaining this heterogeneity in protein populations and discuss the increasing amount of evidence that indicates that the process of structural evolution involves the divergence of protein sequences and structures from one another. We also consider the topic of protein designability, which concerns itself with understanding how a protein's structure influences the number of sequences that can fold successfully into that structure. Understanding and quantifying the relationship between the physical feature of a structure and its designability has been a long-standing goal of the study of protein structure and evolution, and we discuss a number of recent advances that have yielded a promising answer to this question. Finally,
 we review the relatively new field of protein structural phylogeny, an area of study in which information about the distribution of protein structures among different organisms is used to reconstruct the evolutionary relationships between them. Taken together, the work that we review presents an increasingly coherent picture of how these unique polymers have evolved over the course of life on Earth.},
  Institution              = {Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.},
  Keywords                 = {Adaptation, Biological; Evolution, Molecular; Phylogeny; Protein Conformation; Proteins, chemistry/classification/metabolism},
  Owner                    = {ranjan},
  Pmid                     = {17124867},
  Timestamp                = {2009.12.05}
}

@Article{Deeds2005,
  Title                    = {The emergence of scaling in sequence-based physical models of protein evolution.},
  Author                   = {Eric J Deeds and Eugene I Shakhnovich},
  Journal                  = {Biophys J},
  Year                     = {2005},

  Month                    = {Jun},
  Number                   = {6},
  Pages                    = {3905--3911},
  Volume                   = {88},

  Abstract                 = {It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other systems has previously been explained using network growth models that, although motivated by biological processes, do not explicitly consider the underlying physics or biology. In this work we explore a sequence-based model for the evolution protein structures and demonstrate that this model is able to recapitulate the scale-free nature observed in graphs of real protein structures. We find that this model also reproduces other statistical feature of the protein domain graph. This represents, to our knowledge, the first such microscopic, physics-based evolutionary model for a scale-free network of biological importance and as such has strong implications for our understanding of the evolution of protein structures and of other biological 
networks.},
  Institution              = {Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Biophysical Phenomena; Biophysics; Evolution, Molecular; Models, Chemical; Models, Genetic; Models, Molecular; Protein Folding; Protein Structure, Tertiary; Proteins, chemistry/genetics},
  Owner                    = {ranjan},
  Pii                      = {S0006-3495(05)73442-1},
  Pmid                     = {15805176},
  Timestamp                = {2009.12.05}
}

@Article{DeGrado1999,
  Title                    = {De novo design and structural characterization of proteins and metalloproteins.},
  Author                   = {W. F. DeGrado and C. M. Summa and V. Pavone and F. Nastri and A. Lombardi},
  Journal                  = {Annu Rev Biochem},
  Year                     = {1999},
  Pages                    = {779--819},
  Volume                   = {68},

  Abstract                 = {De novo protein design has recently emerged as an attractive approach for studying the structure and function of proteins. This approach critically tests our understanding of the principles of protein folding; only in de novo design must one truly confront the issue of how to specify a protein's fold and function. If we truly understand proteins, it should be possible to design receptors, enzymes, and ion channels from scratch. Further, as this understanding evolves and is further refined, it should be possible to design proteins and biomimetic polymers with properties unprecedented in nature.},
  Institution              = {Johnson Research Foundation, Pennsylvania, Philadelphia, USA. wdegrado@mail.med.upenn.edu},
  Keywords                 = {Metalloproteins, chemistry; Protein Folding; Protein Structure, Secondary; Proteins, chemistry},
  Owner                    = {ranjan},
  Pmid                     = {10872466},
  Timestamp                = {2009.11.27}
}

@Article{Deiana2008,
  Title                    = {Number of natively unfolded proteins scales with genome size},
  Author                   = {Antonio Deiana and Andrea Giansanti},
  Journal                  = {Biophys. and Bioengin. Letters},
  Year                     = {2008},
  Pages                    = {1-7},
  Volume                   = {1},

  Owner                    = {ranjan},
  Timestamp                = {2012.09.26}
}

@Article{Delsuc2005,
  Title                    = {Phylogenomics and the reconstruction of the tree of life.},
  Author                   = {Delsuc, Fr{\'{e}}d{\'{e}}ric and Brinkmann, Henner and Philippe, Herv{\'{e}}},
  Journal                  = {Nat Rev Genet},
  Year                     = {2005},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {361--375},
  Volume                   = {6},

  Abstract                 = {As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.},
  Doi                      = {10.1038/nrg1603},
  Institution              = {Canadian Institute for Advanced Research, Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada.},
  Keywords                 = {Animals; Evolution, Molecular; Genome; Genomics, methods; Phylogeny},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nrg1603},
  Pmid                     = {15861208},
  Timestamp                = {2014.05.18}
}

@Article{Desjarlais1999,
  Title                    = {Side-chain and backbone flexibility in protein core design.},
  Author                   = {J. R. Desjarlais and T. M. Handel},
  Journal                  = {J Mol Biol},
  Year                     = {1999},

  Month                    = {Jul},
  Number                   = {1},
  Pages                    = {305--318},
  Volume                   = {290},

  Abstract                 = {We have developed a computational approach for the design and prediction of hydrophobic cores that includes explicit backbone flexibility. The program consists of a two-stage combination of a genetic algorithm and monte carlo sampling using a torsional model of the protein. Backbone structures are evaluated either by a canonical force-field or a constraining potential that emphasizes the preservation of local geometry. The utility of the method for protein design and engineering is explored by designing three novel hydrophobic core variants of the protein 434 cro. We use the new method to evaluate these and previously designed 434 cro variants, as well as a series of phage T4 lysozyme variants. In order to properly evaluate the influence of backbone flexibility, we have also analyzed the effects of varying amounts of side-chain flexibility on the performance of fixed backbone methods. Comparison of results using a fixed versus flexible backbone reveals that, surprisingly, the 
two methods are almost equivalent in their abilities to predict relative experimental stabilities, but only when full side-chain flexibility is allowed. The prediction of core side-chain structure can vary dramatically between methods. In some, but not all, cases the flexible backbone method is a better predictor of structure. The development of a flexible backbone approach to core design is particularly important for attempts at de novo protein design, where there is no prior knowledge of a precise backbone structure.},
  Institution              = {Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.},
  Keywords                 = {Algorithms; Bacteriophage T4, chemistry; DNA-Binding Proteins; Muramidase, chemistry; Protein Conformation; Protein Denaturation; Repressor Proteins, chemistry; Viral Proteins; Viral Regulatory and Accessory Proteins},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(99)92866-8},
  Pmid                     = {10388574},
  Timestamp                = {2011.01.23}
}

@Article{Desmet2002,
  Title                    = {Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization.},
  Author                   = {Johan Desmet and Jan Spriet and Ignace Lasters},
  Journal                  = {Proteins},
  Year                     = {2002},

  Month                    = {Jul},
  Number                   = {1},
  Pages                    = {31--43},
  Volume                   = {48},

  Abstract                 = {We have developed an original method for global optimization of protein side-chain conformations, called the Fast and Accurate Side-Chain Topology and Energy Refinement (FASTER) method. The method operates by systematically overcoming local minima of increasing order. Comparison of the FASTER results with those of the dead-end elimination (DEE) algorithm showed that both methods produce nearly identical results, but the FASTER algorithm is 100-1000 times faster than the DEE method and scales in a stable and favorable way as a function of protein size. We also show that low-order local minima may be almost as accurate as the global minimum when evaluated against experimentally determined structures. In addition, the new algorithm provides significant information about the conformational flexibility of individual side-chains. We observed that strictly rigid side-chains are concentrated mainly in the core of the protein, whereas highly flexible side-chains are found almost 
exclusively among solvent-oriented residues.},
  Institution              = {AlgoNomics NV, Gent-Zwijnaarde, Belgium. Johan.Desmet@algonomics.com},
  Keywords                 = {Algorithms; Amino Acids, chemistry; Animals; Computational Biology, methods; Crystallography, X-Ray; Models, Molecular; Protein Conformation; Proteins, chemistry; Sensitivity and Specificity; Time Factors},
  Owner                    = {ranjan},
  Pmid                     = {12012335},
  Timestamp                = {2011.01.23}
}

@Article{Destainville2005,
  Title                    = {Random tilings of high symmetry: I. Mean-field theory.},
  Author                   = {Destainville, N. and Widom, M. and Mosseri, R. and Bailly, F.},
  Journal                  = {J. Stat. Phys.},
  Year                     = {2005},
  Pages                    = {799},
  Volume                   = {120},

  File                     = {Destainville2005.pdf:pdfs/Destainville2005.pdf:PDF}
}

@Article{Dhar2010,
  Title                    = {Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding.},
  Author                   = {Apratim Dhar and Antonios Samiotakis and Simon Ebbinghaus and Lea Nienhaus and Dirar Homouz and Martin Gruebele and Margaret S Cheung},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2010},

  Month                    = {Oct},
  Number                   = {41},
  Pages                    = {17586--17591},
  Volume                   = {107},

  Abstract                 = {We combine experiment and computer simulation to show how macromolecular crowding dramatically affects the structure, function, and folding landscape of phosphoglycerate kinase (PGK). Fluorescence labeling shows that compact states of yeast PGK are populated as the amount of crowding agents (Ficoll 70) increases. Coarse-grained molecular simulations reveal three compact ensembles: C (crystal structure), CC (collapsed crystal), and Sph (spherical compact). With an adjustment for viscosity, crowded wild-type PGK and fluorescent PGK are about 15 times or more active in 200?mg/ml Ficoll than in aqueous solution. Our results suggest a previously undescribed solution to the classic problem of how the ADP and diphosphoglycerate binding sites of PGK come together to make ATP: Rather than undergoing a hinge motion, the ADP and substrate sites are already located in proximity under crowded conditions that mimic the in vivo conditions under which the enzyme actually operates. We also 
examine T-jump unfolding of PGK as a function of crowding experimentally. We uncover a nonmonotonic folding relaxation time vs. Ficoll concentration. Theory and modeling explain why an optimum concentration exists for fastest folding. Below the optimum, folding slows down because the unfolded state is stabilized relative to the transition state. Above the optimum, folding slows down because of increased viscosity.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Dhar2010.pdf:PDF},
  Institution              = {Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.},
  Keywords                 = {Binding Sites, genetics; Computer Simulation; Ficoll, chemistry; Fluorescence Resonance Energy Transfer; Kinetics; Models, Chemical; Models, Molecular; Phosphoglycerate Kinase, chemistry/metabolism; Protein Conformation; Protein Folding; Temperature; Viscosity; Yeasts},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {1006760107},
  Pmid                     = {20921368},
  Timestamp                = {2011.11.27}
}

@Article{Dill1997,
  Title                    = {From Levinthal to pathways to funnels.},
  Author                   = {Dill, K. A. and Chan, H. S.},
  Journal                  = {Nat Struct Biol},
  Year                     = {1997},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {10--19},
  Volume                   = {4},

  Abstract                 = {While the classical view of protein folding kinetics relies on phenomenological models, and regards folding intermediates in a structural way, the new view emphasizes the ensemble nature of protein conformations. Although folding has sometimes been regarded as a linear sequence of events, the new view sees folding as parallel microscopic multi-pathway diffusion-like processes. While the classical view invoked pathways to solve the problem of searching for the needle in the haystack, the pathway idea was then seen as conflicting with Anfinsen's experiments showing that folding is pathway-independent (Levinthal's paradox). In contrast, the new view sees no inherent paradox because it eliminates the pathway idea: folding can funnel to a single stable state by multiple routes in conformational space. The general energy landscape picture provides a conceptual framework for understanding both two-state and multi-state folding kinetics. Better tests of these ideas will come when new 
experiments become available for measuring not just averages of structural observables, but also correlations among their fluctuations. At that point we hope to learn much more about the real shapes of protein folding landscapes.},
  Institution              = {Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204, USA. dill@maxwell.ucsf.edu},
  Keywords                 = {Kinetics; Models, Chemical; Protein Folding},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {8989315},
  Timestamp                = {2013.05.01}
}

@Book{Dill2010,
  Title                    = {Molecular driving forces: statistical thermodynamics in biology, chemistry, physics, and nanoscience},
  Author                   = {Dill, Ken and Bromberg, Sarina},
  Publisher                = {Garland Science},
  Year                     = {2010},

  Owner                    = {ranjan},
  Timestamp                = {2015.06.29}
}

@Article{Dima2000,
  Title                    = {Extraction of interaction potentials between amino acids from native protein structures},
  Author                   = {Ruxandra Dima and Giovanni Settanni and Cristian Micheletti and Jayanth Banavar and Amos Maritan},
  Journal                  = {J Chem Phys},
  Year                     = {2000},
  Pages                    = {9151},
  Volume                   = {112},

  Owner                    = {ranjan},
  Timestamp                = {2011.10.24}
}

@Article{Ding2002,
  Title                    = {Direct molecular dynamics observation of protein folding transition state ensemble.},
  Author                   = {Feng Ding and Nikolay V Dokholyan and Sergey V Buldyrev and H. Eugene Stanley and Eugene I Shakhnovich},
  Journal                  = {Biophys J},
  Year                     = {2002},

  Month                    = {Dec},
  Number                   = {6},
  Pages                    = {3525--3532},
  Volume                   = {83},

  Abstract                 = {The concept of the protein transition state ensemble (TSE), a collection of the conformations that have 50\% probability to convert rapidly to the folded state and 50\% chance to rapidly unfold, constitutes the basis of the modern interpretation of protein engineering experiments. It has been conjectured that conformations constituting the TSE in many proteins are the expanded and distorted forms of the native state built around a specific folding nucleus. This view has been supported by a number of on-lattice and off-lattice simulations. Here we report a direct observation and characterization of the TSE by molecular dynamic folding simulations of the C-Src SH3 domain, a small protein that has been extensively studied experimentally. Our analysis reveals a set of key interactions between residues, conserved by evolution, that must be formed to enter the kinetic basin of attraction of the native state.},
  Institution              = {Center for Polymer Studies, Department of Physics, Boston University, Boston, MA 02215, USA. fding@polymer.bu.edu},
  Keywords                 = {Computer Simulation; Energy Transfer; Models, Molecular; Protein Conformation; Protein Denaturation; Protein Engineering, methods; Protein Folding; Protein Structure, Tertiary; Proto-Oncogene Proteins pp60(c-src), chemistry; Temperature; src Homology Domains},
  Owner                    = {ranjan},
  Pii                      = {S0006-3495(02)75352-6},
  Pmid                     = {12496119},
  Timestamp                = {2009.12.05}
}

@Article{Dobrindt2003,
  Title                    = {Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays.},
  Author                   = {Dobrindt, Ulrich and Agerer, Franziska and Michaelis, Kai and Janka, Andreas and Buchrieser, Carmen and Samuelson, Martin and Svanborg, Catharina and Gottschalk, Gerhard and Karch, Helge and Hacker, J\"{o}rg},
  Journal                  = {J Bacteriol},
  Year                     = {2003},

  Month                    = {Mar},
  Number                   = {6},
  Pages                    = {1831--1840},
  Volume                   = {185},

  Abstract                 = {Genomes of prokaryotes differ significantly in size and DNA composition. Escherichia coli is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal E. coli isolates, a whole-genome approach was applied. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic E. coli K-12 strain MG1655 was investigated in 26 E. coli isolates, including various extraintestinal and intestinal pathogenic E. coli isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of E. coli was 
determined using a DNA "pathoarray" developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different E. coli strains. Up to 10\% of the E. coli K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic E. coli are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal E. coli isolates. Based on these results, the conserved E. coli core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among E. coli strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.},
  Keywords                 = {Electrophoresis, Gel, Pulsed-Field; Escherichia coli Infections, microbiology; Escherichia coli Proteins, genetics; Escherichia coli, genetics/pathogenicity; Evolution, Molecular; Genetic Variation; Genome, Bacterial; Humans; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis, methods; Open Reading Frames, genetics; Polymerase Chain Reaction; Sequence Analysis, DNA; Virulence},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {12618447},
  Timestamp                = {2012.09.10}
}

@Article{Doerr2006,
  Title                    = {Widening the protein crystallization bottleneck.},
  Author                   = {Doerr, Allison},
  Journal                  = {Nat Methods},
  Year                     = {2006},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {961},
  Volume                   = {3},

  Abstract                 = {Two recent reports describe simple methods that may help expand the range of proteins amenable to crystallization.},
  Keywords                 = {Binding Sites; Computer Simulation; Crystallization, methods/trends; Dimerization; Models, Chemical; Models, Molecular; Multiprotein Complexes, chemistry/ultrastructure; Protein Binding; Protein Conformation; Proteins, chemistry/ultrastructure},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {17190005},
  Timestamp                = {2013.12.11}
}

@Article{Dokholyan2000,
  Title                    = {Identifying the protein folding nucleus using molecular dynamics.},
  Author                   = {N. V. Dokholyan and S. V. Buldyrev and H. E. Stanley and E. I. Shakhnovich},
  Journal                  = {J Mol Biol},
  Year                     = {2000},

  Month                    = {Mar},
  Number                   = {5},
  Pages                    = {1183--1188},
  Volume                   = {296},

  Abstract                 = {Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model protein into its folded conformation. Amino acid residues participating in those contacts may serve as "accelerator pedals" used by molecular evolution to control protein folding rate.},
  Institution              = {Physics Department, Center for Polymer Studies, Boston, MA 02215, USA.},
  Keywords                 = {Binding Sites; Computer Simulation; Evolution, Molecular; Kinetics; Models, Molecular; Protein Conformation; Protein Denaturation; Protein Folding; Protein Renaturation; Proteins, chemistry/metabolism; Temperature; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(99)93534-9},
  Pmid                     = {10698625},
  Timestamp                = {2009.12.05}
}

@Article{Dokholyan2002,
  Title                    = {Expanding protein universe and its origin from the biological Big Bang.},
  Author                   = {Nikolay V Dokholyan and Boris Shakhnovich and Eugene I Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2002},

  Month                    = {Oct},
  Number                   = {22},
  Pages                    = {14132--14136},
  Volume                   = {99},

  Abstract                 = {The bottom-up approach to understanding the evolution of organisms is by studying molecular evolution. With the large number of protein structures identified in the past decades, we have discovered peculiar patterns that nature imprints on protein structural space in the course of evolution. In particular, we have discovered that the universe of protein structures is organized hierarchically into a scale-free network. By understanding the cause of these patterns, we attempt to glance at the very origin of life.},
  File                     = {Dokholyan2002.pdf:pdfs/Dokholyan2002.pdf:PDF},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA. dokh@med.unc.edu},
  Keywords                 = {Computer Simulation; Evolution, Molecular; Models, Molecular; Protein Structure, Tertiary; Proteins, chemistry},
  Owner                    = {ranjan},
  Pii                      = {202497999},
  Pmid                     = {12384571},
  Timestamp                = {2009.12.05}
}

@Article{Dokholyan2001,
  Title                    = {Understanding hierarchical protein evolution from first principles.},
  Author                   = {N. V. Dokholyan and E. I. Shakhnovich},
  Journal                  = {J Mol Biol},
  Year                     = {2001},

  Month                    = {Sep},
  Number                   = {1},
  Pages                    = {289--307},
  Volume                   = {312},

  Abstract                 = {We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved across protein families. Due to its dynamic nature, the model sheds light on the evolutionary time-scales. By studying the relaxation of the correlation function between consecutive mutations at a given position in proteins, we observe separation of the evolutionary time-scales: at short time intervals families of proteins with similar sequences and structures are formed, while at long time intervals the families of structurally similar proteins that have low sequence similarity are formed. We discuss the evolutionary implications of our model. We provide a "profile" solution to our model and find agreement between predicted patterns of conserved amino acids and those actually observed in nature.},
  Institution              = {Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA. dokh@wild.harvard.edu},
  Keywords                 = {Amino Acid Sequence; Amino Acid Substitution; Conserved Sequence; Models, Molecular; Protein Folding; Proteins, chemistry; Sequence Homology, Amino Acid},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(01)94949-6},
  Pmid                     = {11545603},
  Timestamp                = {2009.12.05}
}

@Article{Dokland1999,
  Title                    = {Scaffolding proteins and their role in viral assembly.},
  Author                   = {Dokland, T.},
  Journal                  = {Cell Mol Life Sci.},
  Year                     = {1999},
  Pages                    = {580--603},
  Volume                   = {56},

  File                     = {Dokland1999.pdf:pdfs/Dokland1999.pdf:PDF}
}

@Article{Dokland1997,
  Title                    = {Structure of a viral procapsid with molecular scaffolding.},
  Author                   = {Dokland,T. and McKenna,R. and Ilag,L.L. and Bowman,B.R. and Incardona,N.L. and Fane,B.A. and Rossmann,M.G.},
  Journal                  = {Nature.},
  Year                     = {1997},
  Number                   = {6648},
  Pages                    = {308-313},
  Volume                   = {389},

  File                     = {Dokland1997.pdf:pdfs/Dokland1997.pdf:PDF}
}

@Article{Doolittle1999,
  Title                    = {Phylogenetic classification and the universal tree.},
  Author                   = {Doolittle, W. F.},
  Journal                  = {Science},
  Year                     = {1999},

  Month                    = {Jun},
  Number                   = {5423},
  Pages                    = {2124--2129},
  Volume                   = {284},

  Abstract                 = {From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a "universal tree of life," taking it as the basis for a "natural" hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be 
represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.},
  Institution              = {Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada. ford@is.dal.ca},
  Keywords                 = {Animals; Archaea, classification/genetics; Bacteria, classification/genetics; Biological Evolution; Eukaryotic Cells, classification; Genes, rRNA; Genome; Phylogeny; RNA, Ribosomal, chemistry/genetics; Recombination, Genetic},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {7604},
  Pmid                     = {10381871},
  Timestamp                = {2012.09.09}
}

@Article{Dosztanyi2006,
  Title                    = {Disorder and sequence repeats in hub proteins and their implications for network evolution.},
  Author                   = {Zsuzsanna Doszt{\'{a}}nyi and Jake Chen and A. Keith Dunker and Istv{\'{a}}n Simon and Peter Tompa},
  Journal                  = {J Proteome Res},
  Year                     = {2006},

  Month                    = {Nov},
  Number                   = {11},
  Pages                    = {2985--2995},
  Volume                   = {5},

  Abstract                 = {Protein interaction networks display approximate scale-free topology, in which hub proteins that interact with a large number of other proteins determine the overall organization of the network. In this study, we aim to determine whether hubs are distinguishable from other networked proteins by specific sequence features. Proteins of different connectednesses were compared in the interaction networks of Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, and Homo sapienswith respect to the distribution of predicted structural disorder, sequence repeats, low complexity regions, and chain length. Highly connected proteins ("hub proteins") contained significantly more of, and greater proportion of, these sequence features and tended to be longer overall as compared to less connected proteins. These sequence features provide two different functional means for realizing multiple interactions: (1) extended interaction surface and (2) flexibility and adaptability,
 providing a mechanism for the same region to bind distinct partners. Our view contradicts the prevailing view that scaling in protein interactomes arose from gene duplication and preferential attachment of equivalent proteins. We propose an alternative evolutionary network specialization process, in which certain components of the protein interactome improved their fitness for binding by becoming longer or accruing regions of disorder and/or internal repeats and have therefore become specialized in network organization.},
  Institution              = {Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, 1518 Budapest, Hungary.},
  Keywords                 = {Amino Acid Sequence; Animals; Caenorhabditis elegans Proteins, chemistry/genetics; Caenorhabditis elegans, genetics; Drosophila Proteins, chemistry/genetics; Drosophila melanogaster, genetics; Evolution, Molecular; Genome; Humans; Nerve Net; Proteins, chemistry/genetics; Repetitive Sequences, Amino Acid; Saccharomyces cerevisiae Proteins, chemistry/genetics; Saccharomyces cerevisiae, genetics; Sequence Homology, Amino Acid},
  Owner                    = {ranjan},
  Pmid                     = {17081050},
  Timestamp                = {2011.03.11}
}

@Article{Dosztanyi2010,
  Title                    = {Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins.},
  Author                   = {Dosztányi, Zsuzsanna and Mészáros, Bálint and Simon, István},
  Journal                  = {Brief Bioinform},
  Year                     = {2010},

  Month                    = {Mar},
  Number                   = {2},
  Pages                    = {225--243},
  Volume                   = {11},

  Abstract                 = {Intrinsically disordered/unstructured proteins exist without a stable three-dimensional (3D) structure as highly flexible conformational ensembles. The available genome sequences revealed that these proteins are surprisingly common and their frequency reaches high proportions in eukaryotes. Due to their vital role in various biological processes including signaling and regulation and their involvement in various diseases, disordered proteins and protein segments are the focus of many biochemical, molecular biological, pathological and pharmaceutical studies. These proteins are difficult to study experimentally because of the lack of unique structure in the isolated form. Their amino acid sequence, however, is available, and can be used for their identification and characterization by bioinformatic tools, analogously to globular proteins. In this review, we first present a small survey of current methods to identify disordered proteins or protein segments, focusing on those that 
are publicly available as web servers. In more detail we also discuss approaches that predict disordered regions and specific regions involved in protein binding by modeling the physical background of protein disorder. In our review we argue that the heterogeneity of disordered segments needs to be taken into account for a better understanding of protein disorder.},
  Doi                      = {10.1093/bib/bbp061},
  Institution              = {Institute of Enzymology, H-1518 Budapest, Hungary.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Computational Biology, methods; Databases, Protein; Evolution, Molecular; Humans; Molecular Sequence Data; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins, chemistry/genetics/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {bbp061},
  Pmid                     = {20007729},
  Timestamp                = {2013.12.08}
}

@Article{Dougan2009,
  Title                    = {Single homopolypeptide chains collapse into mechanically rigid conformations.},
  Author                   = {Dougan L, Li J, Badilla CL, Berne BJ, Fernandez JM},
  Journal                  = {Proc Natl Acad Sci U S A.},
  Year                     = {2009},
  Number                   = {31},
  Pages                    = {12605-12610},
  Volume                   = {106},

  Owner                    = {ranjan},
  Timestamp                = {2010.09.03}
}

@Article{Drexler1981,
  Title                    = {Molecular engineering: An approach to the development of general capabilities for molecular manipulation},
  Author                   = {Drexler,K.E.},
  Journal                  = PNAS,
  Year                     = {1981},
  Number                   = {9},
  Pages                    = {5275-5278},
  Volume                   = {78},

  File                     = {Drexler1981.pdf:pdfs/Drexler1981.pdf:PDF}
}

@Article{drexler2011peptoids,
  Title                    = {Peptoids at the 7th Summit: Toward macromolecular systems engineering},
  Author                   = {Drexler, K Eric},
  Journal                  = {Peptide Science},
  Year                     = {2011},
  Number                   = {5},
  Pages                    = {537--544},
  Volume                   = {96},

  Publisher                = {Wiley Online Library}
}

@Article{DuBay2011,
  Title                    = {Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone},
  Author                   = {DuBay, Kateri H and Bothma, Jacques P and Geissler, Phillip L},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2011},
  Number                   = {9},
  Pages                    = {e1002168},
  Volume                   = {7},

  Owner                    = {ranjan},
  Publisher                = {Public Library of Science},
  Timestamp                = {2016.05.29}
}

@Article{Dunker2013,
  Title                    = {What’s in a name? Why these proteins are intrinsically disordered?},
  Author                   = {Dunker, A.K. and Babu, M. and Barbar, E. and Blackledge, M. and Bondos, S.E. and Doszt\'anyi, Z. and Dyson, H.J. and Forman-Kay, J. and Fuxreiter, M. and Gsponer, J. and Han, K.-H. and Jones, D.T. and Longhi, S. and Metallo, S.J. and Nishikawa, K. and Nussinov, R. and Obradovic, Z. and Pappu, R. and Rost, B. and Selenko, P. and Subramaniam, V. and Sussman, J.L. and Tompa, P. and Uversky, V.N.},
  Journal                  = {Intrinsically Disordered Proteins},
  Year                     = {2013},
  Pages                    = {e24157},
  Volume                   = {1},

  Owner                    = {ranjan},
  Timestamp                = {2013.12.08}
}

@Article{Dunker2005,
  Title                    = {Flexible nets. The roles of intrinsic disorder in protein interaction networks.},
  Author                   = {Dunker, A Keith and Cortese, Marc S. and Romero, Pedro and Iakoucheva, Lilia M. and Uversky, Vladimir N.},
  Journal                  = {FEBS J},
  Year                     = {2005},

  Month                    = {Oct},
  Number                   = {20},
  Pages                    = {5129--5148},
  Volume                   = {272},

  Abstract                 = {Proteins participate in complex sets of interactions that represent the mechanistic foundation for much of the physiology and function of the cell. These protein-protein interactions are organized into exquisitely complex networks. The architecture of protein-protein interaction networks was recently proposed to be scale-free, with most of the proteins having only one or two connections but with relatively fewer 'hubs' possessing tens, hundreds or more links. The high level of hub connectivity must somehow be reflected in protein structure. What structural quality of hub proteins enables them to interact with large numbers of diverse targets? One possibility would be to employ binding regions that have the ability to bind multiple, structurally diverse partners. This trait can be imparted by the incorporation of intrinsic disorder in one or both partners. To illustrate the value of such contributions, this review examines the roles of intrinsic disorder in protein network 
architecture. We show that there are three general ways that intrinsic disorder can contribute: First, intrinsic disorder can serve as the structural basis for hub protein promiscuity; secondly, intrinsically disordered proteins can bind to structured hub proteins; and thirdly, intrinsic disorder can provide flexible linkers between functional domains with the linkers enabling mechanisms that facilitate binding diversity. An important research direction will be to determine what fraction of protein-protein interaction in regulatory networks relies on intrinsic disorder.},
  Doi                      = {10.1111/j.1742-4658.2005.04948.x},
  Institution              = {Department of Biochemistry and Molecular Biology, and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA. kedunker@iupui.edu},
  Keywords                 = {Animals; Binding Sites; Calmodulin, chemistry/metabolism; Cell Physiological Phenomena; Cyclin-Dependent Kinases, chemistry/metabolism; Glycogen Synthase Kinase 3, chemistry/metabolism; HMGA Proteins, chemistry/metabolism; Humans; Models, Biological; Models, Molecular; Protein Binding; Protein Conformation; Protein Structure, Tertiary; Proteins, chemistry/metabolism; Xeroderma Pigmentosum Group A Protein, chemistry/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {EJB4948},
  Pmid                     = {16218947},
  Timestamp                = {2013.12.06}
}

@Article{Dunker2001,
  Title                    = {Intrinsically disordered protein.},
  Author                   = {Dunker, A. K. and Lawson, J. D. and Brown, C. J. and Williams, R. M. and Romero, P. and Oh, J. S. and Oldfield, C. J. and Campen, A. M. and Ratliff, C. M. and Hipps, K. W. and Ausio, J. and Nissen, M. S. and Reeves, R. and Kang, C. and Kissinger, C. R. and Bailey, R. W. and Griswold, M. D. and Chiu, W. and Garner, E. C. and Obradovic, Z.},
  Journal                  = {J Mol Graph Model},
  Year                     = {2001},
  Number                   = {1},
  Pages                    = {26--59},
  Volume                   = {19},

  Abstract                 = {Proteins can exist in a trinity of structures: the ordered state, the molten globule, and the random coil. The five following examples suggest that native protein structure can correspond to any of the three states (not just the ordered state) and that protein function can arise from any of the three states and their transitions. (1) In a process that likely mimics infection, fd phage converts from the ordered into the disordered molten globular state. (2) Nucleosome hyperacetylation is crucial to DNA replication and transcription; this chemical modification greatly increases the net negative charge of the nucleosome core particle. We propose that the increased charge imbalance promotes its conversion to a much less rigid form. (3) Clusterin contains an ordered domain and also a native molten globular region. The molten globular domain likely functions as a proteinaceous detergent for cell remodeling and removal of apoptotic debris. (4) In a critical signaling event, a helix in 
calcineurin becomes bound and surrounded by calmodulin, thereby turning on calcineurin's serine/threonine phosphatase activity. Locating the calcineurin helix within a region of disorder is essential for enabling calmodulin to surround its target upon binding. (5) Calsequestrin regulates calcium levels in the sarcoplasmic reticulum by binding approximately 50 ions/molecule. Disordered polyanion tails at the carboxy terminus bind many of these calcium ions, perhaps without adopting a unique structure. In addition to these examples, we will discuss 16 more proteins with native disorder. These disordered regions include molecular recognition domains, protein folding inhibitors, flexible linkers, entropic springs, entropic clocks, and entropic bristles. Motivated by such examples of intrinsic disorder, we are studying the relationships between amino acid sequence and order/disorder, and from this information we are predicting intrinsic order/disorder from amino acid sequence. The sequence-structure relationships 
indicate that disorder is an encoded property, and the predictions strongly suggest that proteins in nature are much richer in intrinsic disorder than are those in the Protein Data Bank. Recent predictions on 29 genomes indicate that proteins from eucaryotes apparently have more intrinsic disorder than those from either bacteria or archaea, with typically > 30\% of eucaryotic proteins having disordered regions of length > or = 50 consecutive residues.},
  Institution              = {School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA. dunker@mail.wsu.edu},
  Keywords                 = {Models, Molecular; Protein Conformation; Protein Folding; Protein Structure, Tertiary; Proteins, chemistry/genetics/physiology; Structure-Activity Relationship},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S1093-3263(00)00138-8},
  Pmid                     = {11381529},
  Timestamp                = {2013.05.09}
}

@Article{Dunker2008,
  Title                    = {Function and structure of inherently disordered proteins.},
  Author                   = {Dunker, A Keith and Silman, Israel and Uversky, Vladimir N. and Sussman, Joel L.},
  Journal                  = {Curr Opin Struct Biol},
  Year                     = {2008},

  Month                    = {Dec},
  Number                   = {6},
  Pages                    = {756--764},
  Volume                   = {18},

  Abstract                 = {The application of bioinformatics methodologies to proteins inherently lacking 3D structure has brought increased attention to these macromolecules. Here topics concerning these proteins are discussed, including their prediction from amino acid sequence, their enrichment in eukaryotes compared to prokaryotes, their more rapid evolution compared to structured proteins, their organization into specific groups, their structural preferences, their half-lives in cells, their contributions to signaling diversity (via high contents of multiple-partner binding sites, post-translational modifications, and alternative splicing), their distinct functional repertoire compared to that of structured proteins, and their involvement in diseases.},
  Institution              = {Center for Computational Biology and Bioinformatics, Institute for Intrinsically Disordered Protein Research, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, USA.},
  Keywords                 = {Animals; Computational Biology; Disease, etiology; Evolution, Molecular; Humans; Protein Conformation; Protein Folding; Proteins, adverse effects/chemistry/genetics/metabolism; Sequence Analysis, Protein; Structure-Activity Relationship},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0959-440X(08)00151-6},
  Pmid                     = {18952168},
  Timestamp                = {2013.05.09}
}

@Article{Dyall-Smith2003,
  Title                    = {Haloarchaeal viruses: how diverse are they?},
  Author                   = {Dyall-Smith, M. and Tang, S. L. and Bath, C.},
  Journal                  = {Res Microbiol.},
  Year                     = {2003},
  Number                   = {4},
  Pages                    = {309-313},
  Volume                   = {154},

  File                     = {Dyall-Smith2003.pdf:pdfs/Dyall-Smith2003.pdf:PDF}
}

@Article{Dyson2005a,
  Title                    = {Intrinsically unstructured proteins and their functions.},
  Author                   = {H. Jane Dyson and Peter E Wright},
  Journal                  = {Nat Rev Mol Cell Biol},
  Year                     = {2005},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {197--208},
  Volume                   = {6},

  Abstract                 = {Many gene sequences in eukaryotic genomes encode entire proteins or large segments of proteins that lack a well-structured three-dimensional fold. Disordered regions can be highly conserved between species in both composition and sequence and, contrary to the traditional view that protein function equates with a stable three-dimensional structure, disordered regions are often functional, in ways that we are only beginning to discover. Many disordered segments fold on binding to their biological targets (coupled folding and binding), whereas others constitute flexible linkers that have a role in the assembly of macromolecular arrays.},
  Institution              = {Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. dyson@scripps.edu},
  Keywords                 = {CREB-Binding Protein; Humans; Nuclear Proteins, chemistry/genetics/physiology; Nucleic Acids, metabolism; Protein Binding; Protein Processing, Post-Translational; Protein Structure, Tertiary; Proteins, chemistry/physiology; Trans-Activators, chemistry/genetics/physiology; Tumor Suppressor Protein p53, chemistry/physiology},
  Owner                    = {ranjan},
  Pii                      = {nrm1589},
  Pmid                     = {15738986},
  Timestamp                = {2010.05.02}
}

@Article{Dyson2002,
  Title                    = {Coupling of folding and binding for unstructured proteins},
  Author                   = {Dyson, H Jane and Wright, Peter E},
  Journal                  = {Current opinion in structural biology},
  Year                     = {2002},
  Number                   = {1},
  Pages                    = {54--60},
  Volume                   = {12},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.17}
}

@Article{Ebeling1984,
  Title                    = {Diffusion and Reaction in Random Media and Models of Evolution Processes},
  Author                   = {W. Ebeling and A. Engel and B. Esser and R. Feistel},
  Journal                  = {J Stat Phys},
  Year                     = {1984},
  Pages                    = {369-384},
  Volume                   = {37},

  Owner                    = {ranjan},
  Timestamp                = {2011.11.22}
}

@Article{Egel2009,
  Title                    = {Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversy.},
  Author                   = {Egel, Richard},
  Journal                  = {Bioessays},
  Year                     = {2009},

  Month                    = {Oct},
  Number                   = {10},
  Pages                    = {1100--1109},
  Volume                   = {31},

  Abstract                 = {It is commonly presumed that abiotic membranes were colonized by proteins later on. Yet, hydrophobic peptides could have formed primordial protein-dominated membranes on their own. In a metabolism-first context, "autocatalytically closed" sets of statistical peptides could organize a self-maintaining protometabolism, assisted by an unfolding set of ribotide-related cofactors. Pairwise complementary ribotide cofactors may have formed docking guides for stochastic peptide formation, before replicating RNA emerged from this subset. Tidally recurring wet-drying cycles and an early onset of photosynthetic activities are considered most likely to meet the thermodynamic requirements. Conceivably, the earliest peptide-dominated vesicles were engaged in light harvesting, together with isoprenoid-tethered pigments, rather than providing an external boundary. Early on, the bulk of prebiotic organic matter can have formed a contiguous layer covering the mineral sediment, held in place by 
colloidal coherence of a hydrogel matrix. This unconventional scenario assumes a late onset of cellular individualization - perhaps from within, resembling endosporogenesis.},
  Institution              = {Department of Biology, University of Copenhagen Biocenter, Copenhagen, Denmark. regel@bio.ku.dk},
  Keywords                 = {Cell Membrane, chemistry/metabolism; Environment; Evolution, Molecular; Models, Molecular; Models, Theoretical; Peptides, chemistry/metabolism; RNA, genetics/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {19708018},
  Timestamp                = {2012.04.09}
}

@Article{Eggers2001,
  Title                    = {Crowding and hydration effects on protein conformation: a study with sol-gel encapsulated proteins.},
  Author                   = {D. K. Eggers and J. S. Valentine},
  Journal                  = {J Mol Biol},
  Year                     = {2001},

  Month                    = {Dec},
  Number                   = {4},
  Pages                    = {911--922},
  Volume                   = {314},

  Abstract                 = {We are developing an experimental system for testing the effects of macromolecular crowding and molecular confinement on protein structure. In the present study, solvent effects on the secondary structure of two proteins were examined by circular dichroism following encapsulation in the hydrated pores of a silica glass matrix by the sol-gel method. Changes in the unfolded conformations of encapsulated apomyoglobin and reduced serum albumin were analyzed after equilibration with aqueous solutions of natural osmolytes, short-chain alcohols, polyethylene glycol, and a complete series of Hofmeister cations. In many instances, the alpha-helical content of the encapsulated protein was increased by addition of solutes at concentrations that have no effect on the protein in the absence of the glass. The results are discussed from the perspective of water structure. We argue that perturbed water at the silica interface causes an increase in the average free energy of the bulk water phase 
which, consequently, diminishes the strength of the hydrophobic effect inside the glass matrix and destabilizes the conformation of encapsulated proteins. We propose that solutes can increase the strength of the hydrophobic effect and influence folding equilibria without directly interacting with the protein. A hypothesis is provided for the apparent paradox that kosmotropic (strongly water binding) anions favor native protein structure, whereas chaotropic (weakly water binding) cations enhance native protein structure. The encapsulation results suggest that macromolecular crowding and molecular confinement are accompanied by hydration effects that may oppose or potentiate the stabilizing effects of excluded volume on protein structure, depending on the surface chemistry of the crowding agent and its influence on bulk water structure. In the crowded environment of a living cell, excluded volume effects, surface-induced water structure, and compatible solutes are expected to complement the dominant forces in 
protein folding.},
  Institution              = {Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569, USA. eggers@chem.ucla.edu},
  Keywords                 = {Apoproteins, chemistry/metabolism; Cations, metabolism; Circular Dichroism; Detergents, chemistry/metabolism; Glass, chemistry; Humans; Methylamines, metabolism; Models, Chemical; Myoglobin, chemistry/metabolism; Osmolar Concentration; Oxidation-Reduction; Polyethylene Glycols, chemistry/metabolism; Protein Folding; Protein Structure, Secondary; Serum Albumin, chemistry/metabolism; Silicon Dioxide, chemistry; Solvents, metabolism; Substrate Specificity; Thermodynamics; Water, chemistry/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(01)95166-6},
  Pmid                     = {11734007},
  Timestamp                = {2011.11.03}
}

@Article{Eigen1971,
  Title                    = {Molecular self-organization and the early stages of evolution.},
  Author                   = {Eigen, M.},
  Journal                  = {Experientia},
  Year                     = {1971},
  Number                   = {11},
  Pages                    = {149--212},
  Volume                   = {27},

  Keywords                 = {Base Sequence; Biological Evolution; Catalysis; Genetic Code; Kinetics; Models, Biological; Molecular Biology; Mutation; Probability; Selection, Genetic; Templates, Genetic; Thermodynamics; Tyrothricin, biosynthesis},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {5134320},
  Timestamp                = {2012.04.05}
}

@Article{Eisenberg2003,
  Title                    = {The discovery of the $\alpha$-helix and $\beta$-sheet, the principal structural features of proteins},
  Author                   = {Eisenberg, David},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2003},
  Number                   = {20},
  Pages                    = {11207--11210},
  Volume                   = {100},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2013.11.10}
}

@Article{Ellis2001,
  Title                    = {Macromolecular crowding: obvious but underappreciated.},
  Author                   = {R. J. Ellis},
  Journal                  = {Trends Biochem Sci},
  Year                     = {2001},

  Month                    = {Oct},
  Number                   = {10},
  Pages                    = {597--604},
  Volume                   = {26},

  Abstract                 = {Biological macromolecules evolve and function within intracellular environments that are crowded with other macromolecules. Crowding results in surprisingly large quantitative effects on both the rates and the equilibria of interactions involving macromolecules, but such interactions are commonly studied outside the cell in uncrowded buffers. The addition of high concentrations of natural and synthetic macromolecules to such buffers enables crowding to be mimicked in vitro, and should be encouraged as a routine variable to study. The stimulation of protein aggregation by crowding might account for the existence of molecular chaperones that combat this effect. Positive results of crowding include enhancing the collapse of polypeptide chains into functional proteins, the assembly of oligomeric structures and the efficiency of action of some molecular chaperones and metabolic pathways.},
  Institution              = {Dept of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK. jellis@bio.warwick.ac.uk},
  Keywords                 = {Animals; Escherichia coli, chemistry/metabolism; Kinetics; Macromolecular Substances; Models, Biological; Molecular Chaperones, chemistry/metabolism; Proteins, chemistry/metabolism; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0968-0004(01)01938-7},
  Pmid                     = {11590012},
  Timestamp                = {2011.08.12}
}

@Article{Emerson1944,
  Title                    = {The induction of mutations by antibodies},
  Author                   = {Emerson, Sterling},
  Journal                  = {Proceedings of the National Academy of Sciences of the United States of America},
  Year                     = {1944},
  Number                   = {8},
  Pages                    = {179},
  Volume                   = {30},

  Owner                    = {ranjan},
  Publisher                = {National Academy of Sciences},
  Timestamp                = {2013.12.03}
}

@Article{Endres2005,
  Title                    = {A reaction landscape identifies the intermediates critical for self-assembly of virus capsids and other polyhedral structures},
  Author                   = {Endres, D. and Miyahara, M. and Moisant, P. and Zlotnick, A.},
  Journal                  = PS,
  Year                     = {2005},
  Pages                    = {1518--1525},
  Volume                   = {14},

  File                     = {Endres2005.pdf:pdfs/Endres2005.pdf:PDF}
}

@Article{England2003,
  Title                    = {Structural determinant of protein designability.},
  Author                   = {Jeremy L England and Eugene I Shakhnovich},
  Journal                  = {Phys Rev Lett},
  Year                     = {2003},

  Month                    = {May},
  Number                   = {21},
  Pages                    = {218101},
  Volume                   = {90},

  Abstract                 = {Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of low energy in a structure on the eigenvalues of the structure's contact matrix, and then use a Monte Carlo simulation to test the applicability of this analytical result to cubic lattice proteins. We find that the lattice structures with the most low-energy sequences are the same as those predicted by the theory. We argue that, given sufficiently strict requirements for foldability, these structures are the most designable, and we propose a simple means to test whether the results in this paper hold true for real proteins.},
  Institution              = {Cambridge, Massachusetts 02138, USA.},
  Keywords                 = {Amino Acids, chemistry; Models, Chemical; Monte Carlo Method; Protein Conformation; Proteins, chemistry; Structure-Activity Relationship; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {12786593},
  Timestamp                = {2011.10.30}
}

@Article{Eo2010,
  Title                    = {Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles.},
  Author                   = {Soo Hyung Eo and J. Andrew DeWoody},
  Journal                  = {Proc Biol Sci},
  Year                     = {2010},

  Month                    = {Dec},
  Number                   = {1700},
  Pages                    = {3587--3592},
  Volume                   = {277},

  Abstract                 = {Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation-extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO3. Family-by-gene interactions 
were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.},
  Institution              = {Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907-1159, USA. eos@purdue.edu},
  Keywords                 = {Animals; Biodiversity; Birds, classification/genetics; DNA, Mitochondrial, genetics; Evolution, Molecular; Genetic Speciation; Genome, Mitochondrial, genetics; Phylogeny; Reptiles, classification/genetics; Species Specificity},
  Owner                    = {ranjan},
  Pii                      = {rspb.2010.0965},
  Pmid                     = {20610427},
  Timestamp                = {2011.04.26}
}

@Article{Ermekov1986,
  Title                    = {[Clinico-roentgenologic evaluation of the efficacy of extra-intracranial microvascular anastomoses in patients with stenoses in the internal carotid artery system]},
  Author                   = {Zh M Ermekov and A. R. Shakhnovich and Iu M Filatov and G. A. Inauri and T. P. Tissen},
  Journal                  = {Zh Vopr Neirokhir Im N N Burdenko},
  Year                     = {1986},
  Number                   = {1},
  Pages                    = {42--50},

  Abstract                 = {The authors analyse the results of clinical and X-ray examination of 20 patients with stenosing lesions in the system of the internal carotid artery after operations for establishing extra-intracranial microvascular anastomoses (EICMA). Marked stable neurological symptomatology was encountered before the operation in arterial stenosis of a high degree (more than 50\%) and the presence of brain infarctions. In functioning EICMA, evolution of stenoses in the system of the internal carotid arteries was found, which was characterized both by their increase (even to the development of thrombosis) and by their involution. Evolution of the stenoses did not occur if the EICMA failed to function. The operation leads to a less marked character of the neurological symptoms or has no particular effect on their dynamics. Changed amplitude and volume of active movements, muscular tone and strength, as well as of speech function, were found to be the most sensitive indicators of the operation 
efficacy. Regression of the neurologic symptoms after the operation was observed even in extensive brain infarctions and long standing of the disease.},
  Keywords                 = {Adolescent; Adult; Carotid Artery Diseases, diagnosis/therapy; Carotid Artery, Internal; Cerebral Angiography; Cerebral Infarction, complications; Cerebral Revascularization; Constriction, Pathologic, therapy; Diatrizoate Meglumine, adverse effects; Diatrizoate, analogs /&/ derivatives; Female; Follow-Up Studies; Humans; Male; Middle Aged; Tomography, X-Ray Computed},
  Owner                    = {ranjan},
  Pmid                     = {3962547},
  Timestamp                = {2009.12.05}
}

@Article{Espinoza-Fonseca2009,
  Title                    = {Reconciling binding mechanisms of intrinsically disordered proteins},
  Author                   = {Espinoza-Fonseca, L Michel},
  Journal                  = {Biochemical and biophysical research communications},
  Year                     = {2009},
  Number                   = {3},
  Pages                    = {479--482},
  Volume                   = {382},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.21}
}

@Article{Espinoza-Fonseca2012,
  Title                    = {Backbone conformational preferences of an intrinsically disordered protein in solution},
  Author                   = {Espinoza-Fonseca, L Michel and Ilizaliturri-Flores, Ian and Correa-Basurto, Jos{\'e}},
  Journal                  = {Molecular BioSystems},
  Year                     = {2012},
  Number                   = {6},
  Pages                    = {1798--1805},
  Volume                   = {8},

  Owner                    = {ranjan},
  Publisher                = {Royal Society of Chemistry},
  Timestamp                = {2013.11.21}
}

@Article{Euler1752,
  Title                    = {Elementa doctrine solidorum},
  Author                   = {Euler,L.},
  Journal                  = {Novi comm. acad. scientiarum imperialis petropolitanae},
  Year                     = {1752},
  Pages                    = {109--160},
  Volume                   = {4}
}

@Article{Fanning1996,
  Title                    = {Protein-protein interactions: PDZ domain networks.},
  Author                   = {A. S. Fanning and J. M. Anderson},
  Journal                  = {Curr Biol},
  Year                     = {1996},

  Month                    = {Nov},
  Number                   = {11},
  Pages                    = {1385--1388},
  Volume                   = {6},

  Abstract                 = {PDZ domains can dimerize or bind to the carboxyl termini of unrelated proteins. Crystallographic studies demonstrate the structural basis for these interactions, which contribute to the ability of PDZ domains to create networks associated with the plasma membrane.},
  Institution              = {Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520-8019, USA.},
  Keywords                 = {Amino Acid Sequence; Animals; Binding Sites; Humans; Molecular Sequence Data; Molecular Structure; Proteins, chemistry/metabolism},
  Owner                    = {ranjan},
  Pii                      = {S0960-9822(96)00737-3},
  Pmid                     = {8939589},
  Timestamp                = {2009.06.21}
}

@Article{Faraldo-Gomez2007,
  Title                    = {On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases},
  Author                   = {Faraldo-G{\'o}mez, Jos{\'e} D and Roux, Beno{\^\i}t},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2007},
  Number                   = {34},
  Pages                    = {13643--13648},
  Volume                   = {104},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2014.09.02}
}

@Article{Federhen2012,
  Title                    = {The NCBI Taxonomy database.},
  Author                   = {Scott Federhen},
  Journal                  = {Nucleic Acids Res},
  Year                     = {2012},

  Month                    = {Jan},
  Number                   = {Database issue},
  Pages                    = {D136--D143},
  Volume                   = {40},

  __markedentry            = {[ranjan]},
  Abstract                 = {The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC's nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as 
conveniently as possible for our user community.},
  Institution              = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. federhen@ncbi.nlm.nih.gov},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {gkr1178},
  Pmid                     = {22139910},
  Timestamp                = {2012.03.21}
}

@Article{Feig2008,
  Title                    = {Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones?},
  Author                   = {Michael Feig},
  Journal                  = {J. Chem. Theory Comput.},
  Year                     = {2008},
  Pages                    = {1555--1564},
  Volume                   = {4},

  Owner                    = {ranjan},
  Timestamp                = {2012.06.22}
}

@Article{Fenwick2014,
  Title                    = {Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR},
  Author                   = {Fenwick, R Bryn and van den Bedem, Henry and Fraser, James S and Wright, Peter E},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2014},
  Number                   = {4},
  Pages                    = {E445--E454},
  Volume                   = {111},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2014.07.23}
}

@Article{Fermani2012,
  Title                    = {Conformational selection and folding-upon-binding of intrinsically disordered protein CP12 regulate photosynthetic enzymes assembly},
  Author                   = {Fermani, Simona and Trivelli, Xavier and Sparla, Francesca and Thumiger, Anton and Calvaresi, Matteo and Marri, Lucia and Falini, Giuseppe and Zerbetto, Francesco and Trost, Paolo},
  Journal                  = {Journal of Biological Chemistry},
  Year                     = {2012},
  Number                   = {25},
  Pages                    = {21372--21383},
  Volume                   = {287},

  Owner                    = {ranjan},
  Publisher                = {ASBMB},
  Timestamp                = {2013.12.06}
}

@Article{Fernandez2007,
  author      = {Ariel Fern{\'a}ndez},
  title       = {Molecular basis for evolving modularity in the yeast protein interaction network.},
  year        = {2007},
  volume      = {3},
  number      = {11},
  month       = {Nov},
  pages       = {e226},
  abstract    = {Scale-free networks are generically defined by a power-law distribution of node connectivities. Vastly different graph topologies fit this law, ranging from the assortative, with frequent similar-degree node connections, to a modular structure. Using a metric to determine the extent of modularity, we examined the yeast protein network and found it to be significantly self-dissimilar. By orthologous node categorization, we established the evolutionary trend in the network, from an "emerging" assortative network to a present-day modular topology. The evolving topology fits a generic connectivity distribution but with a progressive enrichment in intramodule hubs that avoid each other. Primeval tolerance to random node failure is shown to evolve toward resilience to hub failure, thus removing the fragility often ascribed to scale-free networks. This trend is algorithmically reproduced by adopting a connectivity accretion law that disfavors like-degree connections for large-degree 
nodes. The selective advantage of this trend relates to the need to prevent a failed hub from inducing failure in an adjacent hub. The molecular basis for the evolutionary trend is likely rooted in the high-entropy penalty entailed in the association of two intramodular hubs.},
  file        = {Fernandez2007.pdf:pdfs/Fernandez2007.pdf:PDF},
  institution = {Department of Bioengineering, Rice University, Houston, Texas, United States of America. arifer@rice.edu},
  journal     = {PLoS Comput Biol},
  keywords    = {Base Sequence; Computer Simulation; Evolution, Molecular; Gene Expression Regulation, genetics; Models, Genetic; Molecular Sequence Data; Protein Interaction Mapping, methods; Proteome, genetics; Saccharomyces cerevisiae Proteins, genetics; Saccharomyces cerevisiae, genetics; Signal Transduction, genetics},
  owner       = {ranjan},
  pii         = {07-PLCB-RA-0127},
  pmid        = {17997598},
  timestamp   = {2011.03.11},
}

@Article{Fernandez2011,
  Title                    = {Non-adaptive origins of interactome complexity.},
  Author                   = {Ariel Fern?ndez and Michael Lynch},
  Journal                  = {Nature},
  Year                     = {2011},

  Month                    = {Jun},
  Number                   = {7352},
  Pages                    = {502--505},
  Volume                   = {474},

  Abstract                 = {The boundaries between prokaryotes, unicellular eukaryotes and multicellular eukaryotes are accompanied by orders-of-magnitude reductions in effective population size, with concurrent amplifications of the effects of random genetic drift and mutation. The resultant decline in the efficiency of selection seems to be sufficient to influence a wide range of attributes at the genomic level in a non-adaptive manner. A key remaining question concerns the extent to which variation in the power of random genetic drift is capable of influencing phylogenetic diversity at the subcellular and cellular levels. Should this be the case, population size would have to be considered as a potential determinant of the mechanistic pathways underlying long-term phenotypic evolution. Here we demonstrate a phylogenetically broad inverse relation between the power of drift and the structural integrity of protein subunits. This leads to the hypothesis that the accumulation of mildly deleterious mutations 
in populations of small size induces secondary selection for protein-protein interactions that stabilize key gene functions. By this means, the complex protein architectures and interactions essential to the genesis of phenotypic diversity may initially emerge by non-adaptive mechanisms.},
  Institution              = {Department of Computer Science, The University of Chicago, Chicago, Illinois 60637, USA.},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {nature09992},
  Pmid                     = {21593762},
  Timestamp                = {2011.08.03}
}

@Article{Fernandez2003,
  Title                    = {Protein folding: could hydrophobic collapse be coupled with hydrogen-bond formation?},
  Author                   = {Fern{\`{a}}ndez, Ariel and Kardos, J{\'{o}}zsef and Goto, Yuji},
  Journal                  = {FEBS Lett},
  Year                     = {2003},

  Month                    = {Feb},
  Number                   = {1-3},
  Pages                    = {187--192},
  Volume                   = {536},

  Abstract                 = {A judicious examination of an exhaustive PDB sample of soluble globular proteins of moderate size (N<102) reveals a commensurable relationship between hydrophobic surface burial and number of backbone hydrogen bonds. An analysis of 50,000 conformations along the longest all-atom MD trajectory allows us to infer that not only the hydrophobic collapse is concurrent with the formation of backbone amide-carbonyl hydrogen bonds, they are also dynamically coupled processes. In statistical terms, hydrophobic clustering of the side chains is inevitably conducive to backbone burial and the latter process becomes thermodynamically too costly and kinetically unfeasible without amide-carbonyl hydrogen-bond formation. Furthermore, the desolvation of most hydrogen bonds is exhaustive along the pathway, implying that such bonds guide the collapse process.},
  Institution              = {Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA. ariel@uchicago.edu},
  Keywords                 = {Animals; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Kinetics; Models, Molecular; Protein Conformation; Protein Folding; Protein Structure, Tertiary; Proteins, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0014579303000565},
  Pmid                     = {12586361},
  Timestamp                = {2012.09.26}
}

@Article{Fernandez-Escamilla2004,
  Title                    = {Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins.},
  Author                   = {Ana-Maria Fernandez-Escamilla and Frederic Rousseau and Joost Schymkowitz and Luis Serrano},
  Journal                  = {Nat Biotechnol},
  Year                     = {2004},

  Month                    = {Oct},
  Number                   = {10},
  Pages                    = {1302--1306},
  Volume                   = {22},

  Abstract                 = {We have developed a statistical mechanics algorithm, TANGO, to predict protein aggregation. TANGO is based on the physico-chemical principles of beta-sheet formation, extended by the assumption that the core regions of an aggregate are fully buried. Our algorithm accurately predicts the aggregation of a data set of 179 peptides compiled from the literature as well as of a new set of 71 peptides derived from human disease-related proteins, including prion protein, lysozyme and beta2-microglobulin. TANGO also correctly predicts pathogenic as well as protective mutations of the Alzheimer beta-peptide, human lysozyme and transthyretin, and discriminates between beta-sheet propensity and aggregation. Our results confirm the model of intermolecular beta-sheet formation as a widespread underlying mechanism of protein aggregation. Furthermore, the algorithm opens the door to a fully automated, sequence-based design strategy to improve the aggregation properties of proteins of scientific 
or industrial interest.},
  Keywords                 = {Algorithms; Amino Acid Substitution; Binding Sites; Computer Simulation; Dimerization; Models, Chemical; Models, Molecular; Models, Statistical; Multiprotein Complexes, chemistry; Mutagenesis, Site-Directed; Mutation; Peptides, chemistry; Protein Binding; Protein Conformation; Proteins, chemistry; Structure-Activity Relationship},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nbt1012},
  Pmid                     = {15361882},
  Timestamp                = {2011.08.12}
}

@Article{Ferreira2003,
  Title                    = {Morphological variants of Sindbis virus produced by a mutation in the capsid protein.},
  Author                   = {Ferreira,D. and Hernandez,R. and Horton,M. and Brown,D.T.},
  Journal                  = {Virology.},
  Year                     = {2003},
  Number                   = {1},
  Pages                    = {54--66},
  Volume                   = {307},

  File                     = {Ferreira2003.pdf:pdfs/Ferreira2003.pdf:PDF}
}

@Article{Filatov1985,
  Title                    = {[Effect of extra-intracranial microvascular anastomoses on the evolution of stenoses in the internal carotid artery system]},
  Author                   = {Iu M Filatov and A. R. Shakhnovich and Zh M Ermekov and G. A. Inauri and T. P. Tissen},
  Journal                  = {Zh Vopr Neirokhir Im N N Burdenko},
  Year                     = {1985},
  Number                   = {4},
  Pages                    = {8--13},

  Abstract                 = {Clinical and angiographic examination of 20 patients with stenoses in the system of the internal carotid artery before and after operations for the formation of extra-intracranial microvascular anastomoses (EICMA), and during EICMA functioning demonstrated the evolution of the stenoses. It was characterized both by their increase (even up to the occurrence of thrombosis) and by their regression. No evolution of the stenoses occurred when EICMA failed to function. The character of evolution of the stenosis was determined by its localization. The trend of the evolution was dependent on the etiology of the stenosis. The degree of EICMA functioning differed and was determined by the character of stenosis evolution. With the development of stenosis into thrombosis, the neurological symptom complex was characterized both by marked augmentation followed by regression as well as by the absence of any changes or positive dynamics of the neurological changes.},
  Keywords                 = {Adolescent; Adult; Carotid Artery Diseases, radiography/therapy; Carotid Artery Thrombosis, therapy; Carotid Artery, Internal; Cerebral Revascularization; Collateral Circulation; Constriction, Pathologic, radiography/therapy; Female; Humans; Intracranial Arteriosclerosis, complications; Male; Middle Aged; Rheumatic Fever, complications; Thrombocytopenia, complications},
  Owner                    = {ranjan},
  Pmid                     = {4050248},
  Timestamp                = {2009.12.05}
}

@Article{Fink2005,
  Title                    = {Natively unfolded proteins.},
  Author                   = {Anthony L Fink},
  Journal                  = {Curr Opin Struct Biol},
  Year                     = {2005},

  Month                    = {Feb},
  Number                   = {1},
  Pages                    = {35--41},
  Volume                   = {15},

  Abstract                 = {It is now clear that a significant fraction of eukaryotic genomes encode proteins with substantial regions of disordered structure. In spite of the lack of structure, these proteins nevertheless are functional; many are involved in critical steps of the cell cycle and regulatory processes. In general, intrinsically disordered proteins interact with a target ligand (often DNA) and undergo a structural transition to a folded form when bound. Several features of intrinsically disordered proteins make them well suited to interacting with multiple targets and to cell regulation. New algorithms have been developed to identify disordered regions of proteins and have demonstrated their presence in cancer-associated proteins and proteins regulated by phosphorylation.},
  Institution              = {Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA. enzyme@cats.ucsc.edu},
  Keywords                 = {Binding Sites; Models, Chemical; Models, Molecular; Protein Binding; Protein Conformation; Protein Folding; Proteins, chemistry/classification; Sequence Analysis, Protein, methods; Structure-Activity Relationship},
  Owner                    = {ranjan},
  Pii                      = {S0959-440X(05)00003-5},
  Pmid                     = {15718131},
  Timestamp                = {2009.11.27}
}

@Article{Fischer1984,
  Title                    = {Einfluss der configuration auf die wirkung der enzyme},
  Author                   = {Fischer, E.},
  Journal                  = {Ber Dt Chem Ges},
  Year                     = {1894},
  Pages                    = {2985--2993},
  Volume                   = {27},

  Owner                    = {ranjan},
  Timestamp                = {2013.12.12}
}

@Article{Fitch1990,
  Title                    = {Correcting parsimonious trees for unseen nucleotide substitutions: the effect of dense branching as exemplified by ribonuclease.},
  Author                   = {W. M. Fitch and J. J. Beintema},
  Journal                  = {Mol Biol Evol},
  Year                     = {1990},

  Month                    = {Sep},
  Number                   = {5},
  Pages                    = {438--443},
  Volume                   = {7},

  Abstract                 = {In a study of mammalian ribonuclease evolutionary rates, we applied the Fitch-Bruschi correction to reduce the bias caused by an unequal sampling of taxa in different lineages. The correction was clearly appropriate but only up to a point. The analysis showed that the sampling of taxa within the pecora was sufficiently intense that no correction for unseen, amino acid-changing, nucleotide substitutions was required. It was also found that the ribonuclease gene was duplicated at least twice at the origin of the pecoran branch of the artiodactyls.},
  Institution              = {Department of Ecology and Evolutionary Biology, University of California, Irvine 92717.},
  Keywords                 = {Animals; Biological Evolution; Brain, enzymology; Humans; Phylogeny; Ribonuclease, Pancreatic, genetics; Ribonucleases, genetics; Semen, enzymology},
  Owner                    = {ranjan},
  Pmid                     = {2263194},
  Timestamp                = {2011.04.27}
}

@Article{Fitch1987,
  Title                    = {The evolution of prokaryotic ferredoxins--with a general method correcting for unobserved substitutions in less branched lineages.},
  Author                   = {W. M. Fitch and M. Bruschi},
  Journal                  = {Mol Biol Evol},
  Year                     = {1987},

  Month                    = {Jul},
  Number                   = {4},
  Pages                    = {381--394},
  Volume                   = {4},

  Abstract                 = {Thirty-one bacterial type ferredoxins were examined by means of the parsimony method for their phylogenetic implications. The results show reasonable relationships in that photosynthetic, thermophilic, and desulfovibrio groups are identifiable; but a number of interesting anomalies occur. These include a methanogen sequence that clusters among the desulfovibrios. There are several differences from the phylogeny of Woese. At least two duplications producing paralogous genes are demonstrated, plus the probable existence of two more. The partial internal gene duplication that doubled the length of ferredoxin is confirmed by showing that the probability of the two ancestrally reconstructed halves possessing that much similarity by chance is 10(-7). Howard and co-workers proposed that the two halves of the Azotobacter vinelandii are reversed relative to most other sequences. A phylogeny, drawn with the halves of the azotobacter sequence (and its relatives) reversed produced a tree 
that had only three less nucleotide substitutions than did the tree without their halves reversed. This plus other evidence suggests that the significantly greater similarity observed across rather than within the halves is more likely the result of convergence.},
  Institution              = {Department of Biological Sciences, University of Southern California, Los Angeles 90089-1481.},
  Keywords                 = {Amino Acid Sequence; Bacteria, genetics; Biological Evolution; Ferredoxins, genetics; Models, Genetic; Molecular Sequence Data; Phylogeny; Sequence Homology, Nucleic Acid},
  Owner                    = {ranjan},
  Pmid                     = {3447013},
  Timestamp                = {2011.04.27}
}

@Article{Fitz-Gibbon1999,
  Title                    = {Whole genome-based phylogenetic analysis of free-living microorganisms.},
  Author                   = {Fitz-Gibbon, S. T. and House, C. H.},
  Journal                  = {Nucleic Acids Res},
  Year                     = {1999},

  Month                    = {Nov},
  Number                   = {21},
  Pages                    = {4218--4222},
  Volume                   = {27},

  Abstract                 = {A phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms. Past attempts to reconstruct the evolutionary relation-ships of microorganisms have been limited to sets of genes rather than complete genomes. Despite apparent rampant lateral gene transfer among microorganisms, these results indicate a single robust underlying evolutionary history for these organisms. Broadly, the tree produced is very similar to the small subunit rRNA tree although several additional phylogenetic relationships appear to be resolved, including the relationship of Archaeoglobus to the methanogens studied. This result is in contrast to notions that a robust phylogenetic reconstruction of microorganisms is impossible due to their genomes being composed of an incomprehensible amalgam of genes with complicated histories and suggests that this style of genome-wide 
phylogenetic analysis could become an important method for studying the ancient diversification of life on Earth. Analyses using informational and operational subsets of the genes showed that this 'tree of life' is not dependent on the phylogenetically more consistent informational genes.},
  Institution              = {Department of Microbiology and Molecular Genetics, University of California, Los Angeles, CA 90095-1489, USA. sorel@mbi.ucla.eu},
  Keywords                 = {Computational Biology; Genes, Archaeal, genetics; Genes, Bacterial, genetics; Genes, Fungal, genetics; Genome, Archaeal; Genome, Bacterial; Genome, Fungal; Phylogeny; Saccharomyces cerevisiae, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {gkc610},
  Pmid                     = {10518613},
  Timestamp                = {2012.09.06}
}

@Article{Flegr2010,
  Title                    = {Elastic, not plastic species: frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms.},
  Author                   = {Jaroslav Flegr},
  Journal                  = {Biol Direct},
  Year                     = {2010},
  Pages                    = {2},
  Volume                   = {5},

  Abstract                 = {Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns) in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years.The frozen plasticity theory suggests that sexual species can evolve new adaptations only when their members are genetically uniform, i.e. only after a portion of the population of the original species had split off, balanced on the edge of extinction for several generations, and then undergone rapid expansion. After a short period of time, estimated on the basis of paleontological data to correspond to 1-2\% of the duration of the species, polymorphism accumulates in the gene pool due to frequency-dependent selection; and thus, in each generation, new mutations occur in the presence of different alleles and therefore change their selection coefficients from generation to 
generation. The species ceases to behave in an evolutionarily plastic manner and becomes evolutionarily elastic on a microevolutionary time-scale and evolutionarily frozen on a macroevolutionary time-scale. It then exists in this state until such changes accumulate in the environment that the species becomes extinct.Frozen plasticity theory, which includes the Darwinian model of evolution as a special case--the evolution of species in a plastic state, not only offers plenty of new predictions to be tested, but also provides explanations for a much broader spectrum of known biological phenomena than classic evolutionary theories.This article was reviewed by Rob Knight, Fyodor Kondrashov and Massimo Di Giulio (nominated by David H. Ardell).},
  Institution              = {Department of Philosophy and History of Science, Charles University, Vinicn? 7, CZ-128 44 Praha 2, Czech Republic. flegr@cesnet.cz},
  Keywords                 = {Adaptation, Physiological; Animals; Biological Evolution; Models, Biological; Reproduction, physiology; Selection, Genetic; Sexual Behavior, Animal, physiology},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {1745-6150-5-2},
  Pmid                     = {20067646},
  Timestamp                = {2011.09.15}
}

@Book{Flory1953,
  Title                    = {Principles of polymer chemistry},
  Author                   = {Paul J. Flory},
  Publisher                = {Cornell University Press},
  Year                     = {1953},

  Owner                    = {ranjan},
  Timestamp                = {2014.08.31}
}

@Article{Flory1939,
  Title                    = {Intramolecular reaction between neighboring substituents of vinyl polymers},
  Author                   = {Flory, Paul J},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {1939},
  Number                   = {6},
  Pages                    = {1518--1521},
  Volume                   = {61},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2014.06.02}
}

@Article{Fokine2005,
  Title                    = {A three-dimensional cryo-electron microscopy structure of the bacteriophage phiKZ head.},
  Author                   = {Fokine,A. and Kostyuchenko,V.A. and Efimov,A.V. and Kurochkina,L.P. and Sykilinda,N.N. and Robben,J. and Volckaert,G. and Hoenger,A. and Chipman,P.R. and Battisti,A.J. and Rossmann,M.G. and Mesyanzhinov,V.V.},
  Journal                  = {J Mol Biol.},
  Year                     = {2005},
  Number                   = {1},
  Pages                    = {117-124},
  Volume                   = {352},

  File                     = {Fokine2005.pdf:pdfs/Fokine2005.pdf:PDF}
}

@Article{Fowler2001,
  Title                    = {Spiral codes and Goldberg representations of icosahedral fullerenes and octahedral analogues},
  Author                   = {Fowler, P. W. and Rogers, K. M.},
  Journal                  = {J. Chem. Inf. Comput. Sci.},
  Year                     = {2001},
  Number                   = {1},
  Pages                    = {108--111},
  Volume                   = {41},

  File                     = {Fowler2001.pdf:pdfs/Fowler2001.pdf:PDF}
}

@Article{Fox2014,
  Title                    = {SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures.},
  Author                   = {Fox, Naomi K. and Brenner, Steven E. and Chandonia, John-Marc},
  Journal                  = {Nucleic Acids Res},
  Year                     = {2014},

  Month                    = {Jan},
  Number                   = {Database issue},
  Pages                    = {D304--D309},
  Volume                   = {42},

  Abstract                 = {Structural Classification of Proteins-extended (SCOPe, http://scop.berkeley.edu) is a database of protein structural relationships that extends the SCOP database. SCOP is a manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. Development of the SCOP 1.x series concluded with SCOP 1.75. The ASTRAL compendium provides several databases and tools to aid in the analysis of the protein structures classified in SCOP, particularly through the use of their sequences. SCOPe extends version 1.75 of the SCOP database, using automated curation methods to classify many structures released since SCOP 1.75. We have rigorously benchmarked our automated methods to ensure that they are as accurate as manual curation, though there are many proteins to which our methods cannot be applied. SCOPe is also partially manually curated to correct some errors in SCOP. SCOPe aims to be backward compatible 
with SCOP, providing the same parseable files and a history of changes between all stable SCOP and SCOPe releases. SCOPe also incorporates and updates the ASTRAL database. The latest release of SCOPe, 2.03, contains 59 514 Protein Data Bank (PDB) entries, increasing the number of structures classified in SCOP by 55\% and including more than 65\% of the protein structures in the PDB.},
  Doi                      = {10.1093/nar/gkt1240},
  Institution              = {Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.},
  Keywords                 = {Databases, Protein; Internet; Protein Structure, Tertiary; Proteins, classification; Systems Integration},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {gkt1240},
  Pmid                     = {24304899},
  Timestamp                = {2014.05.11}
}

@Article{Freckleton2002,
  Title                    = {Phylogenetic analysis and comparative data: a test and review of evidence.},
  Author                   = {R. P. Freckleton and P. H. Harvey and M. Pagel},
  Journal                  = {Am Nat},
  Year                     = {2002},

  Month                    = {Dec},
  Number                   = {6},
  Pages                    = {712--726},
  Volume                   = {160},

  Abstract                 = {The question is often raised whether it is statistically necessary to control for phylogenetic associations in comparative studies. To investigate this question, we explore the use of a measure of phylogenetic correlation, lambda, introduced by Pagel (1999), that normally varies between 0 (phylogenetic independence) and 1 (species' traits covary in direct proportion to their shared evolutionary history). Simulations show lambda to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error. Moreover, lambda is robust to incomplete phylogenetic information, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. To assess whether traits generally show phylogenetic associations, we present a quantitative review of 26 published phylogenetic comparative data sets. The data sets include 103 traits and were chosen from the ecological literature 
in which debate about the need for phylogenetic correction has been most acute. Eighty-eight percent of data sets contained at least one character that displayed significant phylogenetic dependence, and 60\% of characters overall (pooled across studies) showed significant evidence of phylogenetic association. In 16\% of tests, phylogenetic correlation could be neither supported nor rejected. However, most of these equivocal results were found in small phylogenies and probably reflect a lack of power. We suggest that the parameter lambda be routinely estimated when analyzing comparative data, since it can also be used simultaneously to adjust the phylogenetic correction in a manner that is optimal for the data set, and we present an example of how this may be done.},
  Institution              = {Department of Zoology, University of Oxford, South Parks Road, Oxford OX13PS, United Kingdom.},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {18707460},
  Timestamp                = {2012.03.09}
}

@Article{Freddolino2006,
  Title                    = {Molecular dynamics simulations of the complete satellite tobacco mosaic virus},
  Author                   = {Freddolino, P. L. and Arkhipov, A. S. and Larson, S. B. and McPherson, A. and Schulten, K.},
  Journal                  = ST,
  Year                     = {2006},
  Number                   = {3},
  Pages                    = {437-449},
  Volume                   = {14},

  File                     = {Freddolino2006.pdf:pdfs/Freddolino2006.pdf:PDF}
}

@Book{Frenkel2001,
  Title                    = {Understanding Molecular Simulation, Second Edition: From Algorithms to Applications},
  Author                   = {Daan Frenkel and Berend Smit},
  Publisher                = {Academic Press},
  Year                     = {2001},
  Edition                  = {2},

  Owner                    = {ranjan},
  Timestamp                = {2012.07.14}
}

@Misc{Frisch2010,
  Title                    = {Gaussian∼09 {R}evision {D}.01},

  Author                   = {M. J. Frisch and G. W. Trucks and H. B. Schlegel and G. E. Scuseria and M. A. Robb and J. R. Cheeseman and G. Scalmani and V. Barone and B. Mennucci and G. A. Petersson and H. Nakatsuji and M. Caricato and X. Li and H. P. Hratchian and A. F. Izmaylov and J. Bloino and G. Zheng and J. L. Sonnenberg and M. Hada and M. Ehara and K. Toyota and R. Fukuda and J. Hasegawa and M. Ishida and T. Nakajima and Y. Honda and O. Kitao and H. Nakai and T. Vreven and Montgomery, {Jr.}, J. A. and J. E. Peralta and F. Ogliaro and M. Bearpark and J. J. Heyd and E. Brothers and K. N. Kudin and V. N. Staroverov and R. Kobayashi and J. Normand and K. Raghavachari and A. Rendell and J. C. Burant and S. S. Iyengar and J. Tomasi and M. Cossi and N. Rega and J. M. Millam and M. Klene and J. E. Knox and J. B. Cross and V. Bakken and C. Adamo and J. Jaramillo and R. Gomperts and R. E. Stratmann and O. Yazyev and A. J. Austin and R. Cammi and C. Pomelli and J. W. Ochterski and R. L. Martin and K. Morokuma and V. G. Zakrzewski and G. A. Voth and P. Salvador and J. J. Dannenberg and S. Dapprich and A. D. Daniels and Ö. Farkas and J. B. Foresman and J. V. Ortiz and J. Cioslowski and D. J. Fox},
  Note                     = {Gaussian Inc. Wallingford CT 2009}
}

@Article{Fuxreiter2012,
  Title                    = {Fuzziness: linking regulation to protein dynamics.},
  Author                   = {Fuxreiter, Monika},
  Journal                  = {Mol Biosyst},
  Year                     = {2012},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {168--177},
  Volume                   = {8},

  Abstract                 = {Proteins are dynamic creatures. Intrinsically disordered proteins (IDPs) function as multiplicity of structures and their activities can only be described by stochastic structure-function relationships. In their complex forms, however, IDPs were thought to lose their plasticity and behave similarly to globular proteins. Although various IDPs indeed fold upon binding, this view is not valid in general. IDPs usually interact with their partners via short motifs, which require malleable environments to function. Consequently, segments of IDPs could retain their disordered state in the complex, a phenomenon termed as fuzziness. Since its recognition, the number of structurally characterized fuzzy complexes, both with protein and DNA, rapidly increases. Here I review recent advances in our understanding of fuzziness. Four basic mechanisms are described how conformationally heterogeneous regions impact specificity or binding affinity of protein complexes. A novel allostery-model is 
proposed, where the regulatory site modulates the conformational equilibrium of the binding interface without adopting a unique structure. Protein-protein interactions, post-translational modifications or alternative splicing of the highly flexible/disordered regions offer further opportunities for regulation and expand the functional repertoire of fuzzy complexes.},
  Doi                      = {10.1039/c1mb05234a},
  Institution              = {Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary. monika@enzim.hu},
  Keywords                 = {Allosteric Regulation; Gene Expression Regulation; Humans; Models, Molecular; Protein Folding; Proteins, chemistry/genetics/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {21927770},
  Timestamp                = {2013.12.14}
}

@Article{Fuxreiter2004,
  Title                    = {Preformed structural elements feature in partner recognition by intrinsically unstructured proteins.},
  Author                   = {Fuxreiter, Monika and Simon, István and Friedrich, Peter and Tompa, Peter},
  Journal                  = {J Mol Biol},
  Year                     = {2004},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {1015--1026},
  Volume                   = {338},

  Abstract                 = {Intrinsically unstructured proteins (IUPs) are devoid of extensive structural order but often display signs of local and limited residual structure. To explain their effective functioning, we reasoned that such residual structure can be crucial in their interactions with their structured partner(s) in a way that preformed structural elements presage their final conformational state. To check this assumption, a database of 24 IUPs with known 3D structures in the bound state has been assembled and the distribution of secondary structure elements and backbone torsion angles have been analysed. The high proportion of residues in coil conformation and with phi, psi angles in the disallowed regions of the Ramachandran map compared to the reference set of globular proteins shows that IUPs are not fully ordered even in their bound form. To probe the effect of partner proteins on IUP folding, inherent conformational preferences of IUP sequences have been assessed by secondary structure 
predictions using the GOR, ALB and PROF algorithms. The accuracy of predicting secondary structure elements of IUPs is similar to that of their partner proteins and is significantly higher than the corresponding values for random sequences. We propose that strong conformational preferences mark regions in IUPs (mostly helices), which correspond to their final structural state, while regions with weak conformational preferences represent flexible linkers between them. In our interpretation, preformed elements could serve as initial contact points, the binding of which facilitates the reeling of the flexible regions onto the template. This finding implies that IUPs draw a functional advantage from preformed structural elements, as they enable their facile, kinetically and energetically less demanding, interaction with their physiological partner.},
  Doi                      = {10.1016/j.jmb.2004.03.017},
  Institution              = {Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary.},
  Keywords                 = {Databases, Protein; Protein Binding, physiology; Protein Structure, Secondary; Proteins, chemistry/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0022283604003079},
  Pmid                     = {15111064},
  Timestamp                = {2013.12.12}
}

@Article{Fuxreiter2012a,
  Title                    = {Fuzzy complexes: a more stochastic view of protein function.},
  Author                   = {Fuxreiter, Monika and Tompa, Peter},
  Journal                  = {Adv Exp Med Biol},
  Year                     = {2012},
  Pages                    = {1--14},
  Volume                   = {725},

  Abstract                 = {Intrinsically disordered proteins (IDPs) are widespread in eukaryotic proteomes and challenge the classical structure-function paradigm that equates a folded 3-D structure with protein function. However, IDPs often function by molecular recognition, in which they bind a partner molecule and undergo "induced folding" or "disorder-to-order transition" upon binding, which apparently suggests that in a functional context IDPs become ordered. Whereas this observation would restore the "prestige" of the classical structure-function paradigm, a closer inspection of the complexes of IDPs reveals that they do not always become fully ordered, but preserve functionally significant disorder in the complex with their binding partner(s). This phenomenon, which we termed "fuzziness", is the ultimate extension of structural disorder to the functional native state of proteins. In this introductory chapter, we outline the most important aspects of fuzziness, such as its structural categories, 
molecular mechanisms of function it mediates and the biological processes, in which it plays a distinguished role. As confirmed by all the other chapters of the book, we will show that new cases of fuzziness pop up at an accelerating pace, underscoring that this phenomenon presents a widespread novel paradigm of protein structure and function.},
  Doi                      = {10.1007/978-1-4614-0659-4_1},
  Institution              = {Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary. monika@enzim.hu},
  Keywords                 = {Animals; Humans; Models, Molecular; Protein Binding; Protein Folding; Protein Structure, Tertiary; Proteins, chemistry/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {22399315},
  Timestamp                = {2013.12.14}
}

@Article{Galvao2006,
  Title                    = {Transcriptional regulators a la carte: engineering new effector specificities in bacterial regulatory proteins},
  Author                   = {Galv{\~a}o, Teca Calcagno and De Lorenzo, Victor},
  Journal                  = {Current opinion in biotechnology},
  Year                     = {2006},
  Number                   = {1},
  Pages                    = {34--42},
  Volume                   = {17},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.12.03}
}

@Article{Geist2013,
  Title                    = {Protonation-dependent conformational variability of intrinsically disordered proteins},
  Author                   = {Geist, Leonhard and Henen, Morkos A and Haiderer, Sandra and Schwarz, Thomas C and Kurzbach, Dennis and Zawadzka-Kazimierczuk, Anna and Saxena, Saurabh and {\.Z}erko, Szymon and Ko{\'z}mi{\'n}ski, Wiktor and Hinderberger, Dariush and others},
  Journal                  = {Protein Science},
  Year                     = {2013},
  Number                   = {9},
  Pages                    = {1196--1205},
  Volume                   = {22},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2015.09.17}
}

@Article{Gillespie1986,
  Title                    = {Natural selection and the molecular clock.},
  Author                   = {J. H. Gillespie},
  Journal                  = {Mol Biol Evol},
  Year                     = {1986},

  Month                    = {Mar},
  Number                   = {2},
  Pages                    = {138--155},
  Volume                   = {3},

  Abstract                 = {This paper concludes that the statistical properties of protein evolution are compatible with a particular model of evolution by natural selection. The argument begins with a statistical description of the molecular clock based on a Poisson process with a randomly varying tick rate. If the time scale of the change of the tick rate of the molecular clock is assumed to be much less than the average time between substitutions, then it is shown that the substitution process must be episodic, with bursts of substitutions being separated by long periods of time with no substitutions. This analysis generalizes the recent work of Gillespie (1984a). The second part of the argument shows that a simple model of evolution by natural selection--one that incorporates a changing environment, the molecular landscape, and a simple form of epistasis--exhibits dynamics that are identical to those inferred from the statistical analysis. This leads to the conclusion that natural selection is a 
viable explanation for protein evolution. In addition, a correction formula for multiple substitutions is given that does not require that the substitution process be a Poisson process, and some comments on the inability of the neutral allele theory to account for the dynamics of the substitution process are presented.},
  Institution              = {Department of Genetics, University of California, Davis 95616.},
  Keywords                 = {Animals; Biological Evolution; Crystallins; Cytochrome c Group; Hemoglobins; Humans; Models, Theoretical; Myoglobin; Probability; Proteins; Ribonucleases; Selection, Genetic; Time Factors},
  Owner                    = {ranjan},
  Pmid                     = {2832690},
  Timestamp                = {2011.04.26}
}

@Article{Gillespie1984,
  Title                    = {The molecular clock may be an episodic clock.},
  Author                   = {J. H. Gillespie},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1984},

  Month                    = {Dec},
  Number                   = {24},
  Pages                    = {8009--8013},
  Volume                   = {81},

  Abstract                 = {It is argued that the apparent constancy of the rate of molecular evolution may be an artifact due to the very slow rate of evolution of individual amino acids. A statistical analysis of protein evolution using a stationary point process as the null hypothesis leads to the conclusion that molecular evolution is episodic, with short bursts of rapid evolution followed by long periods of slow evolution. Such dynamics are incompatible with the neutral allele theory and require a revision of the standard interpretation of the molecular clock.},
  Keywords                 = {Alleles; Amino Acid Sequence; Animals; Biological Evolution; Humans; Models, Genetic; Periodicity; Phylogeny; Proteins, genetics},
  Owner                    = {ranjan},
  Pmid                     = {6595674},
  Timestamp                = {2011.04.26}
}

@Article{Gillespie1984a,
  Title                    = {The status of the neutral theory: the neutral theory of molecular evolution.},
  Author                   = {Gillespie, J. H.},
  Journal                  = {Science},
  Year                     = {1984},

  Month                    = {May},
  Number                   = {4650},
  Pages                    = {732--733},
  Volume                   = {224},

  Doi                      = {10.1126/science.224.4650.732},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {224/4650/732},
  Pmid                     = {17780612},
  Timestamp                = {2013.12.01}
}

@Article{Glansdorff2008,
  Title                    = {The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner.},
  Author                   = {Nicolas Glansdorff and Ying Xu and Bernard Labedan},
  Journal                  = {Biol Direct},
  Year                     = {2008},
  Pages                    = {29},
  Volume                   = {3},

  Abstract                 = {BACKGROUND: Since the reclassification of all life forms in three Domains (Archaea, Bacteria, Eukarya), the identity of their alleged forerunner (Last Universal Common Ancestor or LUCA) has been the subject of extensive controversies: progenote or already complex organism, prokaryote or protoeukaryote, thermophile or mesophile, product of a protracted progression from simple replicators to complex cells or born in the cradle of "catalytically closed" entities? We present a critical survey of the topic and suggest a scenario. RESULTS: LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse. LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to be a significant source of phylogenetic anomalies, i.e. instances where a protein tree 
departs from the SSU-rRNA genealogy; consequently, horizontal gene transfer may not have the rampant character assumed by many. Examining membrane lipids suggest LUCA had sn1,2 ester fatty acid lipids from which Archaea emerged from the outset as thermophilic by "thermoreduction," with a new type of membrane, composed of sn2,3 ether isoprenoid lipids; this occurred without major enzymatic reconversion. Bacteria emerged by reductive evolution from LUCA and some lineages further acquired extreme thermophily by convergent evolution. This scenario is compatible with the hypothesis that the RNA to DNA transition resulted from different viral invasions as proposed by Forterre. Beyond the controversy opposing "replication first" to metabolism first", the predictive arguments of theories on "catalytic closure" or "compositional heredity" heavily weigh in favour of LUCA's ancestors having emerged as complex, self-replicating entities from which a genetic code arose under natural selection. CONCLUSION: Life was born 
complex and the LUCA displayed that heritage. It had the "body "of a mesophilic eukaryote well before maturing by endosymbiosis into an organism adapted to an atmosphere rich in oxygen. Abundant indications suggest reductive evolution of this complex and heterogeneous entity towards the "prokaryotic" Domains Archaea and Bacteria. The word "prokaryote" should be abandoned because epistemologically unsound. REVIEWERS: This article was reviewed by Anthony Poole, Patrick Forterre, and Nicolas Galtier.},
  Institution              = {JM Wiame Research Institute for Microbiology and Vrije Universiteit Brussel, 1 ave E. Gryzon, B-1070 Brussels, Belgium. nglansdo@vub.ac.be},
  Keywords                 = {Archaea, cytology/genetics/metabolism/physiology; Bacteria, cytology/genetics/metabolism; Eukaryotic Cells, cytology/metabolism/physiology; Evolution; Phylogeny; Prokaryotic Cells, cytology/metabolism/physiology},
  Owner                    = {ranjan},
  Pii                      = {1745-6150-3-29},
  Pmid                     = {18613974},
  Timestamp                = {2009.10.01}
}

@Article{Glasner2007,
  Title                    = {Mechanisms of protein evolution and their application to protein engineering.},
  Author                   = {Glasner, Margaret E. and Gerlt, John A. and Babbitt, Patricia C.},
  Journal                  = {Adv Enzymol Relat Areas Mol Biol},
  Year                     = {2007},
  Pages                    = {193--239, xii-xiii},
  Volume                   = {75},

  Abstract                 = {Protein engineering holds great promise for the development of new biosensors, diagnostics, therapeutics, and agents for bioremediation. Despite some remarkable successes in experimental and computational protein design, engineered proteins rarely achieve the efficiency or specificity of natural enzymes. Current protein design methods utilize evolutionary concepts, including mutation, recombination, and selection, but the inability to fully recapitulate the success of natural evolution suggests that some evolutionary principles have not been fully exploited. One aspect of protein engineering that has received little attention is how to select the most promising proteins to serve as templates, or scaffolds, for engineering. Two evolutionary concepts that could provide a rational basis for template selection are the conservation of catalytic mechanisms and functional promiscuity. Knowledge of the catalytic motifs responsible for conserved aspects of catalysis in mechanistically 
diverse superfamilies could be used to identify promising templates for protein engineering. Second, protein evolution often proceeds through promiscuous intermediates, suggesting that templates which are naturally promiscuous for a target reaction could enhance protein engineering strategies. This review explores these ideas and alternative hypotheses concerning protein evolution and engineering. Future research will determine if application of these principles will lead to a protein engineering methodology governed by predictable rules for designing efficient, novel catalysts.},
  Institution              = {Department of Biopharmaceutical Sciences, University of California-San Francisco, San Francisco, CA 94143, USA.},
  Keywords                 = {Binding Sites; Catalysis; Evolution, Molecular; Protein Engineering, methods; Proteins, chemistry/classification/genetics/metabolism; Substrate Specificity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {17124868},
  Timestamp                = {2013.12.09}
}

@Article{Glasner2006,
  Title                    = {Evolution of enzyme superfamilies.},
  Author                   = {Glasner, Margaret E. and Gerlt, John A. and Babbitt, Patricia C.},
  Journal                  = {Curr Opin Chem Biol},
  Year                     = {2006},

  Month                    = {Oct},
  Number                   = {5},
  Pages                    = {492--497},
  Volume                   = {10},

  Abstract                 = {Enzyme evolution is often constrained by aspects of catalysis. Sets of homologous proteins that catalyze different overall reactions but share an aspect of catalysis, such as a common partial reaction, are called mechanistically diverse superfamilies. The common mechanistic steps and structural characteristics of several of these superfamilies, including the enolase, Nudix, amidohydrolase, and haloacid dehalogenase superfamilies have been characterized. In addition, studies of mechanistically diverse superfamilies are helping to elucidate mechanisms of functional diversification, such as catalytic promiscuity. Understanding how enzyme superfamilies evolve is vital for accurate genome annotation, predicting protein functions, and protein engineering.},
  Doi                      = {10.1016/j.cbpa.2006.08.012},
  Institution              = {Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA.},
  Keywords                 = {Binding Sites; Catalysis; Enzyme Activation, physiology; Enzymes, chemistry/physiology; Evolution, Molecular; Molecular Structure},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S1367-5931(06)00117-7},
  Pmid                     = {16935022},
  Timestamp                = {2013.12.09}
}

@Article{Glavin2008,
  Title                    = {Detection of cometary amines in samples returned by Stardust},
  Author                   = {Glavin,D.P. and Dworkin,J.P. and Sandford,S.A.},
  Journal                  = {Meteoritics and planetary science},
  Year                     = {2008},
  Pages                    = {399-413},
  Volume                   = {43},

  Owner                    = {ranjan},
  Timestamp                = {2009.09.21}
}

@Article{Goh2004,
  Title                    = {Conformational changes associated with protein--protein interactions},
  Author                   = {Goh, Chern-Sing and Milburn, Duncan and Gerstein, Mark},
  Journal                  = {Current opinion in structural biology},
  Year                     = {2004},
  Number                   = {1},
  Pages                    = {104--109},
  Volume                   = {14},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.19}
}

@Article{Goldberg1937,
  Title                    = {Class of multi-symmetric polyhedra},
  Author                   = {Goldberg,M.A.},
  Journal                  = {T$\hat{o}$hoku Math. J.},
  Year                     = {1937},
  Pages                    = {104--108},
  Volume                   = {43}
}

@Article{Goldstein1992,
  Title                    = {Protein tertiary structure recognition using optimized Hamiltonians with local interactions.},
  Author                   = {R. A. Goldstein and Z. A. Luthey-Schulten and P. G. Wolynes},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1992},

  Month                    = {Oct},
  Number                   = {19},
  Pages                    = {9029--9033},
  Volume                   = {89},

  Abstract                 = {Protein folding codes embodying local interactions including surface and secondary structure propensities and residue-residue contacts are optimized for a set of training proteins by using spin-glass theory. A screening method based on these codes correctly matches the structure of a set of test proteins with proteins of similar topology with 100\% accuracy, even with limited sequence similarity between the test proteins and the structural homologs and the absence of any structurally similar proteins in the training set.},
  Institution              = {School of Chemical Sciences, University of Illinois, Urbana 61801.},
  Keywords                 = {Amino Acids; Animals; Humans; Mathematics; Models, Theoretical; Protein Folding; Protein Structure, Tertiary},
  Owner                    = {ranjan},
  Pmid                     = {1409599},
  Timestamp                = {2010.01.26}
}

@Article{Goldstein2006,
  Title                    = {Observations of amino acid gain and loss during protein evolution are explained by statistical bias.},
  Author                   = {Richard A Goldstein and David D Pollock},
  Journal                  = {Mol Biol Evol},
  Year                     = {2006},

  Month                    = {Jul},
  Number                   = {7},
  Pages                    = {1444--1449},
  Volume                   = {23},

  Abstract                 = {The authors of a recent manuscript in "Nature" claim to have discovered "universal trends" of amino acid gain and loss in protein evolution. Here, we show that this universal trend can be simply explained by a bias that is unavoidable with the 3-taxon trees used in the original analysis. We demonstrate that a rigorously reversible equilibrium model, when analyzed with the same methods as the "Nature" manuscript, yields identical (and in this case, clearly erroneous) conclusions. A main source of the bias is the division of the sequence data into "informative" and "noninformative" sites, which favors the observation of certain transitions.},
  Institution              = {Division of Mathematical Biology, National Institute of Medical Research, Mill Hill, London, United Kingdom. richard.goldstein@nimr.mrc.ac.uk},
  Keywords                 = {Algorithms; Amino Acid Substitution; Amino Acids, genetics; Bias (Epidemiology); Computational Biology, methods; Evolution, Molecular; Models, Genetic; Proteins, chemistry/genetics},
  Owner                    = {ranjan},
  Pii                      = {msl010},
  Pmid                     = {16698770},
  Timestamp                = {2010.06.26}
}

@Article{Goldstein1994,
  Title                    = {Efficient rotamer elimination applied to protein side-chains and related spin glasses.},
  Author                   = {R. F. Goldstein},
  Journal                  = {Biophys J},
  Year                     = {1994},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {1335--1340},
  Volume                   = {66},

  Abstract                 = {Folded proteins and spin glasses share various properties, such as seemingly random interactions between residues (spins), and one might presume that some generic behaviors of spin glasses would also be exhibited in a general way by proteins. But a comparison here shows that the side-chain conformation systems of apo-myoglobin and lysozyme are qualitatively different from specific closely related spin glass systems. This difference is manifest in the number of rotamers that can be identified as definitely not contributing to the global energy minimum. This identification is effected by using a significantly enhanced version of the Dead End Elimination theorem (Desmet, J., M. De Maeyer, B. Hazes, and I. Lasters. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature. 356:539-542), which is much more effective and efficient in eliminating rotamers. In several cases (for proteins, although not for spin glasses) this improved Dead End 
Elimination theorem succeeded in identifying the absolute global minimum of rotamer conformations, with no statistical uncertainty. The difference between protein and spin glass is due to correlations between the interactions of one residue pair with another pair, and probably will play an important role in the thermodynamic behavior of the protein system.},
  Institution              = {Computer Center, University of Illinois at Chicago 60612-7352.},
  Keywords                 = {Algorithms; Apoproteins, chemistry; Biophysical Phenomena; Biophysics; Glass; Models, Chemical; Molecular Structure; Muramidase, chemistry; Myoglobin, chemistry; Protein Conformation; Proteins, chemistry; Spin Labels; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {S0006-3495(94)80923-3},
  Pmid                     = {8061189},
  Timestamp                = {2011.01.23}
}

@Book{Golub1989,
  Title                    = {Matrix computations},
  Author                   = {Golub, G. and Van Loan, C. F.},
  Publisher                = {The Johns Hopkins University Press},
  Year                     = {1989},

  Address                  = {Baltimore, USA},
  Edition                  = {2nd}
}

@Article{Gonzalez1996,
  Title                    = {Buried polar residues and structural specificity in the GCN4 leucine zipper.},
  Author                   = {L. Gonzalez and D. N. Woolfson and T. Alber},
  Journal                  = {Nat Struct Biol},
  Year                     = {1996},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {1011--1018},
  Volume                   = {3},

  Abstract                 = {A conserved asparagine (Asn 16) buried in the interface of the GCN4 leucine zipper selectively favours the parallel, dimeric, coiled-coil structure. To test if other polar residues confer oligomerization specificity, the structural effects of Gln and Lys substitutions for Asn 16 were characterized. Like the wild-type peptide, the Asn 16Lys mutant formed exclusively dimers. In contrast, Gln 16, despite its chemical similarity to Asn, allowed the peptide to form both dimers and trimers. The Gln 16 side chain was accommodated by qualitatively different interactions in the dimer and trimer crystal structures. These findings demonstrate that the structural selectivity of polar residues results not only from the burial of polar atoms, but also depends on the complementarity of the side-chain stereochemistry with the surrounding structural environment.},
  Institution              = {Department of Molecular and Cell Biology, University of California Berkeley 94720-3206, USA.},
  Keywords                 = {Amino Acid Sequence; DNA-Binding Proteins; Dimerization; Fungal Proteins, chemistry/genetics; Leucine Zippers; Models, Molecular; Molecular Sequence Data; Mutation; Protein Conformation; Protein Kinases, chemistry/genetics; Saccharomyces cerevisiae Proteins},
  Owner                    = {ranjan},
  Pmid                     = {8946854},
  Timestamp                = {2010.09.22}
}

@Article{Goodman2007,
  Title                    = {Foldamers as versatile frameworks for the design and evolution of function},
  Author                   = {Goodman, Catherine M and Choi, Sungwook and Shandler, Scott and DeGrado, William F},
  Journal                  = {Nature chemical biology},
  Year                     = {2007},
  Number                   = {5},
  Pages                    = {252--262},
  Volume                   = {3},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2014.06.11}
}

@Article{Goodsell2000,
  Title                    = {Structural symmetry and protein function.},
  Author                   = {Goodsell, D. S. and Olson, A. J.},
  Journal                  = {Annu Rev Biophys Biomol Struct},
  Year                     = {2000},
  Pages                    = {105--153},
  Volume                   = {29},

  Abstract                 = {The majority of soluble and membrane-bound proteins in modern cells are symmetrical oligomeric complexes with two or more subunits. The evolutionary selection of symmetrical oligomeric complexes is driven by functional, genetic, and physicochemical needs. Large proteins are selected for specific morphological functions, such as formation of rings, containers, and filaments, and for cooperative functions, such as allosteric regulation and multivalent binding. Large proteins are also more stable against denaturation and have a reduced surface area exposed to solvent when compared with many individual, smaller proteins. Large proteins are constructed as oligomers for reasons of error control in synthesis, coding efficiency, and regulation of assembly. Symmetrical oligomers are favored because of stability and finite control of assembly. Several functions limit symmetry, such as interaction with DNA or membranes, and directional motion. Symmetry is broken or modified in many forms: 
quasisymmetry, in which identical subunits adopt similar but different conformations; pleomorphism, in which identical subunits form different complexes; pseudosymmetry, in which different molecules form approximately symmetrical complexes; and symmetry mismatch, in which oligomers of different symmetries interact along their respective symmetry axes. Asymmetry is also observed at several levels. Nearly all complexes show local asymmetry at the level of side chain conformation. Several complexes have reciprocating mechanisms in which the complex is asymmetric, but, over time, all subunits cycle through the same set of conformations. Global asymmetry is only rarely observed. Evolution of oligomeric complexes may favor the formation of dimers over complexes with higher cyclic symmetry, through a mechanism of prepositioned pairs of interacting residues. However, examples have been found for all of the crystallographic point groups, demonstrating that functional need can drive the evolution of any symmetry.},
  Doi                      = {10.1146/annurev.biophys.29.1.105},
  Institution              = {Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA. goodsell@scripps.edu, olson@scripps.edu},
  Keywords                 = {Allosteric Site; Animals; DNA, metabolism; Dimerization; Models, Biological; Models, Molecular; Protein Binding; Protein Conformation; Protein Structure, Tertiary; Proteins, chemistry/physiology; Structure-Activity Relationship},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {29/1/105},
  Pmid                     = {10940245},
  Timestamp                = {2014.04.28}
}

@Article{Gopinath1994,
  Title                    = {Primary structure of sesbania mosaic virus coat protein: its implications to the assembly and architecture of the virus.},
  Author                   = {Gopinath, K. and Sundareshan, S. and Bhuvaneswari, M. and Karande, A. and Murthy, M. R. and Nayudu, M. V. and Savithri, H. S.},
  Journal                  = {Indian J. Biochem. Biophys.},
  Year                     = {1994},
  Pages                    = {322},
  Volume                   = {31}
}

@Article{Gordon1999,
  Title                    = {Branch-and-terminate: a combinatorial optimization algorithm for protein design.},
  Author                   = {D. B. Gordon and S. L. Mayo},
  Journal                  = {Structure},
  Year                     = {1999},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {1089--1098},
  Volume                   = {7},

  Abstract                 = {Several deterministic and stochastic combinatorial optimization algorithms have been applied to computational protein design and homology modeling. As structural targets increase in size, however, it has become necessary to find more powerful methods to address the increased combinatorial complexity.We present a new deterministic combinatorial search algorithm called 'Branch-and-Terminate' (B&T), which is derived from the Branch-and-Bound search method. The B&T approach is based on the construction of an efficient but very restrictive bounding expression, which is used for the search of a combinatorial tree representing the protein system. The bounding expression is used both to determine the optimal organization of the tree and to perform a highly effective pruning procedure named 'termination'. For some calculations, the B&T method rivals the current deterministic standard, dead-end elimination (DEE), sometimes finding the solution up to 21 times faster. A more significant 
feature of the B&T algorithm is that it can provide an efficient way to complete the optimization of problems that have been partially reduced by a DEE algorithm.The B&T algorithm is an effective optimization algorithm when used alone. Moreover, it can increase the problem size limit of amino acid sidechain placement calculations, such as protein design, by completing DEE optimizations that reach a point at which the DEE criteria become inefficient. Together the two algorithms make it possible to find solutions to problems that are intractable by either algorithm alone.},
  Institution              = {Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California, 91125, USA.},
  Keywords                 = {Algorithms; Models, Molecular; Molecular Structure; Protein Engineering, methods; Proteins, chemical synthesis/chemistry},
  Owner                    = {ranjan},
  Pii                      = {st7902},
  Pmid                     = {10508778},
  Timestamp                = {2011.01.23}
}

@Article{Gotoh2008,
  Title                    = {Metabolism of odd-numbered fatty acids and even-numbered fatty acids in mouse.},
  Author                   = {Gotoh, Naohiro and Moroda, Koichiro and Watanabe, Hiroyuki and Yoshinaga, Kazuaki and Tanaka, Miho and Mizobe, Hoyo and Ichioka, Kenji and Tokairin, Shigeru and Wada, Shun},
  Journal                  = {J Oleo Sci},
  Year                     = {2008},
  Number                   = {5},
  Pages                    = {293--299},
  Volume                   = {57},

  Abstract                 = {Fatty acids are converted into energy via beta-oxidation. Although almost all natural occurring fatty acids are even-numbered, there are some odd-numbered fatty acids too. The details of the metabolism rate of odd-numbered fatty acids, however, are not clear. In the present study, we simultaneously administered a triacylglycerol containing four types of labeled even-numbered (palmitic acid and stearic acid) and odd-numbered (pentadecanoic acid and heptadecanoic acid) fatty acids to mice to compare the rates of their metabolism. The rates of metabolism were evaluated based on the accumulation of the labeled fatty acids in the small intestine epithelium, liver, and epididymal fat. Odd-numbered fatty acids accumulated mainly in the epididymal fat. In contrast, there was no accumulation of even-numbered fatty acids observed in the small intestine epithelium, liver, or epididymal fat. These results suggest that odd-numbered fatty acids might not be favorable substrates for beta-
oxidation-related enzymes.},
  Institution              = {Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan.},
  Keywords                 = {Animals; Body Weight, drug effects; Fatty Acids, administration /&/ dosage/chemistry/metabolism/pharmacology; Male; Mice; Mice, Inbred ICR; Organ Size, drug effects; Tissue Extracts, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {JST.JSTAGE/jos/57.293},
  Pmid                     = {18391478},
  Timestamp                = {2014.01.17}
}

@Article{Gough2005,
  Title                    = {Convergent evolution of domain architectures (is rare).},
  Author                   = {Gough, Julian},
  Journal                  = {Bioinformatics},
  Year                     = {2005},

  Month                    = {Apr},
  Number                   = {8},
  Pages                    = {1464--1471},
  Volume                   = {21},

  Abstract                 = {In this paper, we shall examine the evolution of domain architectures across 62 genomes of known phylogeny including all kingdoms of life. We look in particular at the possibility of convergent evolution, with a view to determining the extent to which the architectures observed in the genomes are due to functional necessity or evolutionary descent. We used domains of known structure, because from this and other information we know their evolutionary relationships. We use a range of methods including phylogenetic grouping, sequence similarity/alignment, mutation rates and comparative genomics to approach this difficult problem from several angles.Although we do not claim an exhaustive analysis, we conclude that between 0.4 and 4\% of sequences are involved in convergent evolution of domain architectures, and expect the actual number to be close to the lower bound. We also made two incidental observations, albeit on a small sample: the events leading to convergent evolution appear 
to be random with no functional or structural preferences, and changes in the number of tandem repeat domains occur more readily than changes which alter the domain composition.The principal conclusion is that the observed domain architectures of the sequences in the genomes are driven by evolutionary descent rather than functional necessity.gough@supfam.org.},
  Institution              = {RIKEN Genomic Sciences Centre, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. gough@supfam.org},
  Keywords                 = {Conserved Sequence; Evolution, Molecular; Genetic Variation, genetics; Phylogeny; Protein Structure, Tertiary; Proteins, chemistry/genetics; Sequence Alignment, methods; Sequence Analysis, Protein, methods; Sequence Homology, Amino Acid; Structure-Activity Relationship},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {bti204},
  Pmid                     = {15585523},
  Timestamp                = {2012.10.18}
}

@Article{Govindarajan1996,
  Title                    = {Why are some proteins structures so common?},
  Author                   = {S. Govindarajan and R. A. Goldstein},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1996},

  Month                    = {Apr},
  Number                   = {8},
  Pages                    = {3341--3345},
  Volume                   = {93},

  Abstract                 = {Many biological proteins are observed to fold into one of a limited number of structural motifs. By considering the requirements imposed on proteins by their need to fold rapidly, and the ease with which such requirements can be fulfilled as a function of the native structure, we can explain why certain structures are repeatedly observed among proteins with negligible sequence similarity. This work has implications for the understanding of protein sequence structure relationships as well as protein evolution.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Govindarajan1996.pdf:PDF},
  Institution              = {Department of Chemistry, University of Michigan, Ann Arbor 48109-1055, USA.},
  Keywords                 = {Evolution, Molecular; Models, Chemical; Molecular Structure; Protein Folding; Proteins, chemistry/genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {8622938},
  Timestamp                = {2011.10.30}
}

@Article{Grunbaum1999,
  Title                    = {Acoptic Polyhedra. In: Advances in Discrete and Computational Geometry},
  Author                   = {Gr\"{u}nbaum, B.},
  Journal                  = {Contemp. Math.},
  Year                     = {1999},
  Pages                    = {163--199},
  Volume                   = {223},

  File                     = {:pdfs/Grunbaum1999.pdf:PDF}
}

@Book{Grunbaum1986,
  Title                    = {Tilings and patterns},
  Author                   = {Gr\"{u}nbaum, B. and Shephard, G. C.},
  Publisher                = {W. H. Freeman},
  Year                     = {1986},

  Address                  = {New York, USA},
  Edition                  = {2nd}
}

@Article{Gruanbaum1980,
  Title                    = {Tilings with congruent tiles},
  Author                   = {Gr\"{u}nbaum, B. and Shephard, G. C.},
  Journal                  = BullAMS,
  Year                     = {1981},
  Pages                    = {951},
  Volume                   = {3},

  File                     = {Gruanbaum1980.pdf:pdfs/Gruanbaum1980.pdf:PDF}
}

@Article{Grunbaum1980,
  Title                    = {Tilings with congruent tiles.},
  Author                   = {Gr\"{u}nbaum, B. and Shephard, G. C.},
  Journal                  = {Bull. Amer. Math. Soc. N.S.},
  Year                     = {1980},
  Pages                    = {951--973},
  Volume                   = {3}
}

@Article{Grimes1998,
  Title                    = {The atomic structure of the bluetongue virus core.},
  Author                   = {Grimes, J.M. and Burroughs, J.N. and Gouet, P. and Diprose, J.M. and Malby, R. and Zi?ntara, S. and Mertens, P.P. and Stuart, D.I.},
  Journal                  = {Nature.},
  Year                     = {1998},
  Number                   = {6701},
  Pages                    = {470-478},
  Volume                   = {395},

  File                     = {Grimes1998.pdf:pdfs/Grimes1998.pdf:PDF}
}

@Article{Grosberg1986,
  Title                    = {[A theory of heteropolymers with frozen random primary structure: properties of the globular state, coil-globule transitions and possible biophysical applications]},
  Author                   = {A. Iu Grosberg and E. I. Shakhnovich},
  Journal                  = {Biofizika},
  Year                     = {1986},
  Number                   = {6},
  Pages                    = {1045--1057},
  Volume                   = {31},

  Abstract                 = {A new approach to the problem of correspondence between primary structures of polypeptides and their tertiary structures is presented. This approach is based on the following statement of the problem: what will be the statistical properties of tertiary structures provided that the statistical properties of primary structures (e. g. the ratio of polar and unpolar residues) are given? It is discussed whether such statement is useful for the investigation of the prebiological evolution and protein folding. It is emphasized that the basic point here is to determine the configurational entropy of the chain, i. e., the number of foldings which lead to a given density distribution space. Hence, the auxiliary problem of the ideal heteropolymer collapse in the external field is considered. This problem is investigated numerically in the case when the field is localized in the small region in space. It is shown that such geometrical characteristics as the size of a globule are not 
sensitive to the details of primary structure when the chain is a random coil, and become sensitive to such details in the opposite globular case. These characteristics in the globular state can be described by the stable probability distribution function which does not depend upon chain length. Geometric characteristics of the chain exhibit especially strong dependence upon the primary structure in the region of coil-globule transition which is of the second order for the ensemble of chains.},
  Keywords                 = {Amino Acid Sequence; Biopolymers; Evolution; Macromolecular Substances; Models, Biological; Protein Conformation; Proteins},
  Owner                    = {ranjan},
  Pmid                     = {3801519},
  Timestamp                = {2009.12.05}
}

@Article{Grottesi1998,
  Title                    = {The conformation of peptide thymosin alpha 1 in solution and in a membrane-like environment by circular dichroism and NMR spectroscopy. A possible model for its interaction with the lymphocyte membrane.},
  Author                   = {A. Grottesi and M. Sette and T. Palamara and G. Rotilio and E. Garaci and M. Paci},
  Journal                  = {Peptides},
  Year                     = {1998},
  Number                   = {10},
  Pages                    = {1731--1738},
  Volume                   = {19},

  Abstract                 = {The 28-residue peptide thymosin alpha1 was studied by circular dichroism and two-dimensional NMR. Circular dichroism indicates that thymosin alpha1 in water solution does not assume a preferred conformation, while in the presence of small unilamellar vesicles of dimiristoylphosphatidylcholine and dimiristoylphosphatidic acid (10:1) and in sodium dodecyl sulphate, it assumes a partly structured conformation. Presence of zinc ions produces similar effects. In a more hydrophobic environment like a solution of a mixed solvent water-2,2,2 trifluoroethanol, it adopts a structured conformation. NMR spectra indicated that in this mixture as solvent, thymosin alpha1 has a structure characterized by two regions. A beta-turn is present between residue 5 and residue 8, while the region between residues 17 and 24 shows an alpha helix conformation. These changes of conformation in different environments may be considered structural requirements in the steps of its interaction with the 
lymphocyte membrane. In fact, these conformational changes may correspond to the first event of the mechanism of lymphocyte activation in the immune response modulation by thymosin alpha1.},
  Institution              = {Department of Chemical Science and Technology, University of Rome Tor Vergata, Italy.},
  Keywords                 = {Adjuvants, Immunologic, chemistry/metabolism; Cell Membrane, chemistry/metabolism; Circular Dichroism; Lymphocytes, chemistry; Membranes, Artificial; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; Thymosin, analogs /&/ derivatives/chemistry/metabolism},
  Owner                    = {ranjan},
  Pii                      = {S0196978198001326},
  Pmid                     = {9880079},
  Timestamp                = {2010.04.15}
}

@Article{Gu1998,
  Title                    = {Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria.},
  Author                   = {Gu, X. and Hewett-Emmett, D. and Li, W. H.},
  Journal                  = {Genetica},
  Year                     = {1998},
  Number                   = {1-6},
  Pages                    = {383--391},
  Volume                   = {102-103},

  Abstract                 = {The relationship between change in genomic GC content and protein evolution in bacteria was studied by simple correlational analysis (at the genus level) and by Felsenstein's (1985) independent contrast test. We first used the dnaA gene in bacteria as an example to show (1) that the amino acid composition of a protein can be dramatically affected by mutational pressure (the genomic GC content), (2) that surprisingly, deleting relatively closely-related genera may increase rather than decrease the correlation between genomic GC content and amino acid composition, and (3) that most unexpectedly, as the genomic GC content increases, both strongly hydrophobic and strongly hydrophilic amino acids tend to change to ambivalent amino acids, suggesting that the majority of these amino acid substitutions are not caused by positive Darwinian selection. These patterns were then also shown to hold for the 14 other genes studied, indicating their generality for the evolution of bacterial 
proteins. As directional mutation pressure can affect the amino acid composition of proteins, it may mislead phylogenetic inference, even if protein instead of DNA sequences are used.},
  Institution              = {Human Genetics Center, SPH, University of Texas, Houston 77225, USA.},
  Keywords                 = {Amino Acids, analysis; Bacteria, genetics; Bacterial Proteins, chemistry/genetics; Base Composition; Base Sequence; Codon, genetics; Evolution, Molecular; Genes, Bacterial; Mutation; Phylogeny},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9720290},
  Timestamp                = {2012.09.27}
}

@Article{Gunasekaran1998,
  Title                    = {Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals},
  Author                   = {Gunasekaran, K and Nagarajaram, HA and Ramakrishnan, C and Balaram, P},
  Journal                  = {Journal of molecular biology},
  Year                     = {1998},
  Number                   = {5},
  Pages                    = {917--932},
  Volume                   = {275},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2016.06.02}
}

@Article{Guoying1980,
  Title                    = {The geochemistry of n-alkanes with an even-odd predominance in the Tertiary Shahejie Formation of northern China},
  Author                   = {Shen Guoying and Fan Shanfa and Lin Dehan and Su Nengxian and Zhou Hongming},
  Journal                  = {Physics and Chemistry of the Earth},
  Year                     = {1980},

  Month                    = {Jan},
  Pages                    = {115-121},
  Volume                   = {12},

  Doi                      = {10.1016/0079-1946(79)90093-4},
  Owner                    = {ranjan},
  Publisher                = {Elsevier },
  Timestamp                = {2014.01.17}
}

@Article{Gutierrez2011,
  Title                    = {Protein amino acid composition: a genomic signature of encephalization in mammals.},
  Author                   = {Humberto Gutierrez and Atahualpa Castillo and Jimena Monzon and Araxi O Urrutia},
  Journal                  = {PLoS One},
  Year                     = {2011},
  Number                   = {11},
  Pages                    = {e27261},
  Volume                   = {6},

  Abstract                 = {Large brains relative to body size represent an evolutionarily costly adaptation as they are metabolically expensive and demand substantial amounts of time to reach structural and functional maturity thereby exacerbating offspring mortality while delaying reproductive age. In spite of its cost and adaptive impact, no genomic features linked to brain evolution have been found. By conducting a genome-wide analysis in all 37 fully sequenced mammalian genomes, we show that encephalization is significantly correlated with overall protein amino acid composition. This correlation is not a by-product of changes in nucleotide content, lifespan, body size, absolute brain size or genome size; is independent of phylogenetic effects; and is not restricted to brain expressed genes. This is the first report of a relationship between this fundamental and complex trait and changes in protein AA usage, possibly reflecting the high selective demands imposed by the process of encephalization across 
mammalian lineages.},
  Institution              = {Instituto de Fisiologia Celular, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria, Mexico City, Mexico. hgutierrez@ifc.unam.mx},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {PONE-D-11-15351},
  Pmid                     = {22132093},
  Timestamp                = {2012.03.09}
}

@Article{Gutin1993,
  Title                    = {Ground state of random copolymers and the discrete random energy model},
  Author                   = {Gutin,A.M. and Shakhnovich,E.I},
  Journal                  = {J. Chem. Phys.},
  Year                     = {1993},
  Pages                    = {8174-8177},
  Volume                   = {98},

  Abstract                 = {We propose and investigate a modification of the random energy model where the energies of different states are still independent random values but may take only discrete values. This model appears naturally in studies of random heteropolymers with monomers of two types. We calculate the probability that the ground state of such a polymer is nondegenerate and test this result against a lattice model of a heteropolymer with exhaustively enumerated conformations. The theory is in excellent agreement with numerical experiment. Our results imply that the lower the energy of the ground state the less probable that it is degenerate. The probability of degeneracy decays exponentially as ground state energy decreases.},
  File                     = {Gutin1993.pdf:pdfs/Gutin1993.pdf:PDF},
  Owner                    = {ranjan},
  Timestamp                = {2009.12.06}
}

@Article{Gutin1995,
  Title                    = {Evolution-like selection of fast-folding model proteins.},
  Author                   = {A. M. Gutin and V. I. Abkevich and E. I. Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1995},

  Month                    = {Feb},
  Number                   = {5},
  Pages                    = {1282--1286},
  Volume                   = {92},

  Abstract                 = {We propose an algorithm providing sequences of model proteins with rapid folding into a given target (native) conformation. This algorithm is applied to a chain of 27 residues on a cubic lattice. It generates sequences with folding 2 orders of magnitude faster than that of the practically random starting sequence. Thermodynamic analysis shows that the increase in speed is matched by an increase in stability: the evolved sequences are much more stable in their native conformation than the initial random sequence. The unfolding temperature for evolved sequences is slightly higher than the simulation temperature, bearing direct correspondence to the relatively low stability of real proteins.},
  Institution              = {Harvard University, Department of Chemistry, Cambridge, MA 02138.},
  Keywords                 = {Algorithms; Kinetics; Monte Carlo Method; Peptides, chemistry; Protein Folding; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {7877968},
  Timestamp                = {2009.12.05}
}

@Article{Gutin1995a,
  Title                    = {Is burst hydrophobic collapse necessary for protein folding?},
  Author                   = {A. M. Gutin and V. I. Abkevich and E. I. Shakhnovich},
  Journal                  = {Biochemistry},
  Year                     = {1995},

  Month                    = {Mar},
  Number                   = {9},
  Pages                    = {3066--3076},
  Volume                   = {34},

  Abstract                 = {Folding of the lattice model of proteins is studied using Monte Carlo simulation. The amino acid sequence is designed to have a pronounced energy minimum for a given target (native) conformation. Our simulations reveal two possible scenarios. When the overall attraction between residues dominates, we find that folding to the native conformation is preceded by a rapid collapse into a burst intermediate which is a compact but structureless globule. Then, after a much longer time, an all-or-none transition from the globule to the native conformation occurs. In contrast, when the overall attraction is not strong, we do not observe a burst collapse stage. Instead, we find an all-or-none transition directly from the coil to the native conformation. Both scenarios yield comparable rates of folding. On the basis of these findings we discuss the role of intermediates in thermodynamics and kinetics of protein folding.},
  File                     = {Gutin1995a.pdf:pdfs/Gutin1995a.pdf:PDF},
  Institution              = {Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138.},
  Keywords                 = {Amino Acid Sequence; Computer Simulation; Kinetics; Models, Chemical; Molecular Sequence Data; Monte Carlo Method; Protein Conformation; Protein Folding; Protein Structure, Secondary; Proteins, chemistry; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {7893719},
  Timestamp                = {2010.01.18}
}

@Article{Guvench2011,
  Title                    = {CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.},
  Author                   = {Guvench, Olgun and Mallajosyula, Sairam S. and Raman, E Prabhu and Hatcher, Elizabeth and Vanommeslaeghe, Kenno and Foster, Theresa J. and Jamison, 2nd, Francis W and Mackerell, Jr, Alexander D},
  Journal                  = {J Chem Theory Comput},
  Year                     = {2011},

  Month                    = {Oct},
  Number                   = {10},
  Pages                    = {3162--3180},
  Volume                   = {7},

  Abstract                 = {Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid (Neu5Ac) are important components of eukaryotic glycans. The present work details development of force-field parameters for these monosaccharides and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N-linkages to asparagine sidechains. The force field development protocol was designed to explicitly yield parameters that are compatible with the existing CHARMM additive force field for proteins, nucleic acids, lipids, carbohydrates, and small molecules. Therefore, when combined with previously developed parameters for pyranose and furanose monosaccharides, for glycosidic linkages between monosaccharides, and for proteins, the present set of parameters enables the molecular simulation of a wide variety of biologically-important molecules such as complex 
carbohydrates and glycoproteins. Parametrization included fitting to quantum mechanical (QM) geometries and conformational energies of model compounds, as well as to QM pair interaction energies and distances of model compounds with water. Parameters were validated in the context of crystals of relevant monosaccharides, as well NMR and/or x-ray crystallographic data on larger systems including oligomeric hyaluronan, sialyl Lewis X, O- and N-linked glycopeptides, and a lectin:sucrose complex. As the validated parameters are an extension of the CHARMM all-atom additive biomolecular force field, they further broaden the types of heterogeneous systems accessible with a consistently-developed force-field model.},
  Institution              = {Department of Pharmaceutical Sciences, University of New England College of Pharmacy, Portland, Maine 04103.},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {22125473},
  Timestamp                = {2012.06.21}
}

@Article{Hagan2006,
  Title                    = {Dynamic pathways for viral capsid assembly},
  Author                   = {Hagan, M. F. and Chandler, D.},
  Journal                  = BPJ,
  Year                     = {2006},
  Pages                    = {42--54},
  Volume                   = {91},

  File                     = {Hagan2006.pdf:pdfs/Hagan2006.pdf:PDF}
}

@Book{Haile1997,
  Title                    = {Molecular Dynamics Simulation: Elementary Methods},
  Author                   = {J. M. Haile},
  Publisher                = {Wiley-Interscience},
  Year                     = {1997},

  Owner                    = {ranjan},
  Timestamp                = {2012.07.14}
}

@Article{Hall2005,
  Title                    = {Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae.},
  Author                   = {Hall, Charles and Brachat, Sophie and Dietrich, Fred S.},
  Journal                  = {Eukaryot Cell},
  Year                     = {2005},

  Month                    = {Jun},
  Number                   = {6},
  Pages                    = {1102--1115},
  Volume                   = {4},

  Abstract                 = {The genomes of the hemiascomycetes Saccharomyces cerevisiae and Ashbya gossypii have been completely sequenced, allowing a comparative analysis of these two genomes, which reveals that a small number of genes appear to have entered these genomes as a result of horizontal gene transfer from bacterial sources. One potential case of horizontal gene transfer in A. gossypii and 10 potential cases in S. cerevisiae were identified, of which two were investigated further. One gene, encoding the enzyme dihydroorotate dehydrogenase (DHOD), is potentially a case of horizontal gene transfer, as shown by sequencing of this gene from additional bacterial and fungal species to generate sufficient data to construct a well-supported phylogeny. The DHOD-encoding gene found in S. cerevisiae, URA1 (YKL216W), appears to have entered the Saccharomycetaceae after the divergence of the S. cerevisiae lineage from the Candida albicans lineage and possibly since the divergence from the A. gossypii lineage.
 This gene appears to have come from the Lactobacillales, and following its acquisition the endogenous eukaryotic DHOD gene was lost. It was also shown that the bacterially derived horizontally transferred DHOD is required for anaerobic synthesis of uracil in S. cerevisiae. The other gene discussed in detail is BDS1, an aryl- and alkyl-sulfatase gene of bacterial origin that we have shown allows utilization of sulfate from several organic sources. Among the eukaryotes, this gene is found in S. cerevisiae and Saccharomyces bayanus and appears to derive from the alpha-proteobacteria.},
  Institution              = {Department of Molecular Genetics and Microbiology, Duke University Medical Center (DUMC) 289 CARL Building, Box 3568, Durham, NC 27710, USA.},
  Keywords                 = {Amino Acid Sequence; Bayes Theorem; Crosses, Genetic; Evolution, Molecular; Fungal Proteins, chemistry; Gene Transfer, Horizontal; Genes, Fungal; Genetic Complementation Test; Genome, Fungal; Molecular Sequence Data; Oxidoreductases Acting on CH-CH Group Donors, genetics; Phylogeny; Saccharomyces cerevisiae, genetics/growth /&/ development; Saccharomycetales, genetics; Sequence Analysis, DNA; Sequence Homology, Amino Acid; Sulfatases, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {4/6/1102},
  Pmid                     = {15947202},
  Timestamp                = {2012.09.10}
}

@Article{Halle2002,
  Title                    = {Flexibility and packing in proteins},
  Author                   = {Halle, Bertil},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2002},
  Number                   = {3},
  Pages                    = {1274--1279},
  Volume                   = {99},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2014.08.20}
}

@Article{Hammer2008,
  Title                    = {Amyloids: friend or foe?},
  Author                   = {Hammer, Neal D and Wang, Xuan and McGuffie, Bryan A and Chapman, Matthew R},
  Journal                  = {Journal of Alzheimer's disease},
  Year                     = {2008},
  Number                   = {4},
  Pages                    = {407--419},
  Volume                   = {13},

  Owner                    = {ranjan},
  Publisher                = {IOS Press},
  Timestamp                = {2015.04.08}
}

@InProceedings{Hammersley1961,
  Title                    = {The number of polygons on a lattice},
  Author                   = {Hammersley, JM},
  Booktitle                = {Proc. Camb. Phil. Soc},
  Year                     = {1961},
  Organization             = {Cambridge Univ Press},
  Pages                    = {516--523},
  Volume                   = {57},

  Owner                    = {ranjan},
  Timestamp                = {2013.07.06}
}

@Article{Hammersley1962,
  Title                    = {Further results on the rate of convergence to the connective constant of the hypercubical lattice},
  Author                   = {Hammersley, JM and Welsh, DJA},
  Journal                  = {The Quarterly Journal of Mathematics},
  Year                     = {1962},
  Number                   = {1},
  Pages                    = {108--110},
  Volume                   = {13},

  Owner                    = {ranjan},
  Publisher                = {Oxford Univ Press},
  Timestamp                = {2013.07.06}
}

@Article{Hammersley1954,
  Title                    = {Poor man's monte carlo},
  Author                   = {Hammersley, John M and Morton, K William},
  Journal                  = {Journal of the Royal Statistical Society. Series B (Methodological)},
  Year                     = {1954},
  Pages                    = {23--38},

  Owner                    = {ranjan},
  Publisher                = {JSTOR},
  Timestamp                = {2013.07.06}
}

@Article{Hammes1964,
  Title                    = {Mechanism of enzyme catalysis},
  Author                   = {Hammes, Gordon G},
  Year                     = {1964},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2013.07.20}
}

@Article{Hanczyc2007,
  Title                    = {Fatty acid chemistry at the oil-water interface: self-propelled oil droplets.},
  Author                   = {Martin M Hanczyc and Taro Toyota and Takashi Ikegami and Norman Packard and Tadashi Sugawara},
  Journal                  = {J Am Chem Soc},
  Year                     = {2007},

  Month                    = {Aug},
  Number                   = {30},
  Pages                    = {9386--9391},
  Volume                   = {129},

  Abstract                 = {Fatty acids have been investigated as boundary structures to construct artificial cells due to their dynamic properties and phase transitions. Here we have explored the possibility that fatty acid systems also demonstrate movement. An oil phase was loaded with a fatty acid anhydride precursor and introduced to an aqueous fatty acid micelle solution. The oil droplets showed autonomous, sustained movement through the aqueous media. Internal convection created a positive feedback loop, and the movement of the oil droplet was sustained as convection drove fresh precursor to the surface to become hydrolyzed. As the system progressed, more surfactant was produced and some of the oil droplets transformed into supramolecular aggregates resembling multilamellar vesicles. The oil droplets also moved directionally within chemical gradients and exhibited a type of chemotaxis.},
  Institution              = {ProtoLife Srl, Parco Vega, Via della Liberta 12, Marghera, Venice, Italy.},
  Keywords                 = {Chemotaxis, physiology; Fatty Acids, chemistry; Liposomes, chemistry; Micelles; Microscopy; Oils, chemistry; Oleic Acid, chemistry; Phase Transition; Solutions, chemistry; Surface Properties; Surface-Active Agents, chemistry; Water, chemistry; Wettability},
  Owner                    = {ranjan},
  Pmid                     = {17616129},
  Timestamp                = {2011.05.13}
}

@Article{Hao2006,
  Title                    = {The fate of laterally transferred genes: life in the fast lane to adaptation or death.},
  Author                   = {Hao, Weilong and Golding, G Brian},
  Journal                  = {Genome Res},
  Year                     = {2006},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {636--643},
  Volume                   = {16},

  Abstract                 = {Large-scale genome arrangement plays an important role in bacterial genome evolution. A substantial number of genes can be inserted into, deleted from, or rearranged within genomes during evolution. Detecting or inferring gene insertions/deletions is of interest because such information provides insights into bacterial genome evolution and speciation. However, efficient inference of genome events is difficult because genome comparisons alone do not generally supply enough information to distinguish insertions, deletions, and other rearrangements. In this study, homologous genes from the complete genomes of 13 closely related bacteria were examined. The presence or absence of genes from each genome was cataloged, and a maximum likelihood method was used to infer insertion/deletion rates according to the phylogenetic history of the taxa. It was found that whole gene insertions/deletions in genomes occur at rates comparable to or greater than the rate of nucleotide substitution and 
that higher insertion/deletion rates are often inferred to be present at the tips of the phylogeny with lower rates on more ancient interior branches. Recently transferred genes are under faster and relaxed evolution compared with more ancient genes. Together, this implies that many of the lineage-specific insertions are lost quickly during evolution and that perhaps a few of the genes inserted by lateral transfer are niche specific.},
  Institution              = {Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.},
  Keywords                 = {Adaptation, Physiological; Bacillaceae, genetics; Bayes Theorem; Death; Evolution, Molecular; Gene Transfer, Horizontal; Genome, Bacterial; Likelihood Functions; Mutagenesis, Insertional; Phylogeny; Sequence Deletion; Species Specificity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {16/5/636},
  Pmid                     = {16651664},
  Timestamp                = {2012.09.07}
}

@Article{Harrison1978,
  Title                    = {Tomato bushy stunt virus at 2.9 $\mbox{\AA}$ resolution},
  Author                   = {Harrison,S.C. and Olson,A.J. and Schutt,C.E. and Winkler,F.K. and Bricogne,G.},
  Journal                  = {Nature},
  Year                     = {1978},
  Pages                    = {368--373},
  Volume                   = {276},

  File                     = {Harrison1978.pdf:pdfs/Harrison1978.pdf:PDF},
  Owner                    = {ranjan},
  Timestamp                = {2009.08.19}
}

@Article{Harrison1996,
  Title                    = {Peptide-surface association: the case of PDZ and PTB domains.},
  Author                   = {S. C. Harrison},
  Journal                  = {Cell},
  Year                     = {1996},

  Month                    = {Aug},
  Number                   = {3},
  Pages                    = {341--343},
  Volume                   = {86},

  Institution              = {Howard Hughes Medical Institute Children's Hospital, Boston, Massachusetts 02115, USA.},
  Keywords                 = {Amino Acid Sequence; Animals; Binding Sites; Humans; Molecular Sequence Data; Protein Binding, physiology; Protein Structure, Secondary; Proteins, chemistry/metabolism; Signal Transduction},
  Owner                    = {ranjan},
  Pii                      = {S0092-8674(00)80105-1},
  Pmid                     = {8756715},
  Timestamp                = {2009.07.07}
}

@InBook{Hart2006,
  Title                    = {Principles of population genetics},
  Author                   = {Daniel L. Hartl and Andrew G. Clark},
  Chapter                  = {Molecular population genetics},
  Pages                    = {317-386},
  Publisher                = {Sinauer Associates, Inc. Publishers},
  Year                     = {2006},
  Edition                  = {4th},

  Owner                    = {ranjan},
  Timestamp                = {2010.12.12}
}

@Article{Haxton2014,
  Title                    = {Hierarchical assembly of peptoid nanosheets catalyzed by an air-water interface},
  Author                   = {Haxton, Thomas and Sanii, Babak and Olivier, Gloria and Mannige, Ranjan and Proulx, Caroline and Cho, Andrew and Zuckermann, Ronald and Whitelam, Stephen},
  Journal                  = {Bulletin of the American Physical Society},
  Year                     = {2014},
  Volume                   = {59},

  Owner                    = {ranjan},
  Publisher                = {APS},
  Timestamp                = {2015.04.08}
}

@Article{Haxtoncgmethodspaper,
  Title                    = {Modeling sequence-specific polymers using anisotropic coarse-grained sites allows quantitative comparison with experiment},
  Author                   = {Thomas K. Haxton and Ranjan V. Mannige and Ronald N. Zuckermann and Stephen Whitelam},
  Journal                  = {In preparation},
  Year                     = {2014},

  Owner                    = {ranjan},
  Timestamp                = {2014.07.29}
}

@Article{Haynes2006,
  Title                    = {Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes.},
  Author                   = {Chad Haynes and Christopher J Oldfield and Fei Ji and Niels Klitgord and Michael E Cusick and Predrag Radivojac and Vladimir N Uversky and Marc Vidal and Lilia M Iakoucheva},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2006},

  Month                    = {Aug},
  Number                   = {8},
  Pages                    = {e100},
  Volume                   = {2},

  Abstract                 = {Recent proteome-wide screening approaches have provided a wealth of information about interacting proteins in various organisms. To test for a potential association between protein connectivity and the amount of predicted structural disorder, the disorder propensities of proteins with various numbers of interacting partners from four eukaryotic organisms (Caenorhabditis elegans, Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens) were investigated. The results of PONDR VL-XT disorder analysis show that for all four studied organisms, hub proteins, defined here as those that interact with > or = 10 partners, are significantly more disordered than end proteins, defined here as those that interact with just one partner. The proportion of predicted disordered residues, the average disorder score, and the number of predicted disordered regions of various lengths were higher overall in hubs than in ends. A binary classification of hubs and ends into ordered and 
disordered subclasses using the consensus prediction method showed a significant enrichment of wholly disordered proteins and a significant depletion of wholly ordered proteins in hubs relative to ends in worm, fly, and human. The functional annotation of yeast hubs and ends using GO categories and the correlation of these annotations with disorder predictions demonstrate that proteins with regulation, transcription, and development annotations are enriched in disorder, whereas proteins with catalytic activity, transport, and membrane localization annotations are depleted in disorder. The results of this study demonstrate that intrinsic structural disorder is a distinctive and common characteristic of eukaryotic hub proteins, and that disorder may serve as a determinant of protein interactivity.},
  File                     = {Haynes2006.pdf:pdfs/Haynes2006.pdf:PDF},
  Institution              = {Laboratory of Statistical Genetics, The Rockefeller University, New York, New York, USA.},
  Keywords                 = {Amino Acids, chemistry; Animals; Caenorhabditis elegans Proteins, chemistry/classification/genetics/metabolism; Caenorhabditis elegans, chemistry/genetics/metabolism; Carrier Proteins, chemistry/classification/genetics/metabolism; Computational Biology; Drosophila Proteins, chemistry/classification/genetics/metabolism; Drosophila melanogaster, chemistry/genetics/metabolism; Hu Paraneoplastic Encephalomyelitis Antigens, chemistry/classification/genetics/metabolism; Humans; Ligases, chemistry/classification/genetics/metabolism; Models, Molecular; Protein Binding; Protein Structure, Tertiary; Saccharomyces cerevisiae Proteins, chemistry/classification/genetics/metabolism; Saccharomyces cerevisiae, chemistry/genetics/metabolism},
  Owner                    = {ranjan},
  Pii                      = {06-PLCB-RA-0152R2},
  Pmid                     = {16884331},
  Timestamp                = {2011.03.11}
}

@Article{Hayward2014,
  Title                    = {Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides},
  Author                   = {Hayward, Steven and Leader, David P and Al-Shubailly, Fawzia and Milner-White, E James},
  Journal                  = {Proteins: Structure, Function, and Bioinformatics},
  Year                     = {2014},
  Number                   = {2},
  Pages                    = {230--239},
  Volume                   = {82},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2015.11.15}
}

@Article{Hayward2008,
  Title                    = {The geometry of $\alpha$-sheet: Implications for its possible function as amyloid precursor in proteins},
  Author                   = {Hayward, Steven and Milner-White, E James},
  Journal                  = {Proteins: Structure, Function, and Bioinformatics},
  Year                     = {2008},
  Number                   = {1},
  Pages                    = {415--425},
  Volume                   = {71},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2015.11.15}
}

@Article{Hazy2009,
  Title                    = {Limitations of induced folding in molecular recognition by intrinsically disordered proteins.},
  Author                   = {Hazy, Eszter and Tompa, Peter},
  Journal                  = {Chemphyschem},
  Year                     = {2009},

  Month                    = {Jul},
  Number                   = {9-10},
  Pages                    = {1415--1419},
  Volume                   = {10},

  Abstract                 = {Intrinsically disordered proteins (IDPs) exist and function without well-defined three-dimensional structures, thus they defy the classical structure-function paradigm. These proteins are common in proteomes, and they carry out essential functions often related to signalling and regulation of transcription. Herein, the experimental evidence for their lack of structure and the major functional benefits that structural disorder confers, are surveyed. It is shown that IDPs often function by molecular recognition, in which either short motifs, or domain-sized disordered segments are used for partner recognition. In both cases, the binding segment undergoes induced folding and it attains an ordered structure. This folding-upon-binding scenario suggests that the function of IDPs can be interpreted in terms of the static structural view of the classical paradigm. New developments in the field, however, suggest that folding upon binding is limited, and many IDPs preserve a significant 
level of disorder in the bound state, a phenomenon termed fuzziness. In addition, IDPs may structurally adapt to different partners with different functional outcomes, resulting in promiscuity in function termed moonlighting. It is suggested that a new model describing the structure-function relationship of IDPs has to encompass such structural and functional promiscuity inherent in the disordered state of IDPs.},
  Doi                      = {10.1002/cphc.200900205},
  Institution              = {Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P.O. Box 7, 1518 Budapest, Hungary.},
  Keywords                 = {Computational Biology; Protein Conformation; Protein Folding; Proteins, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {19462392},
  Timestamp                = {2013.12.08}
}

@Article{He2009,
  Title                    = {Predicting intrinsic disorder in proteins: an overview},
  Author                   = {He, Bo and Wang, Kejun and Liu, Yunlong and Xue, Bin and Uversky, Vladimir N and Dunker, A Keith},
  Journal                  = {Cell research},
  Year                     = {2009},
  Number                   = {8},
  Pages                    = {929--949},
  Volume                   = {19},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2013.07.30}
}

@Article{Hedges2014,
  Title                    = {Growth of equilibrium structures built from a large number of distinct component types},
  Author                   = {Hedges, Lester O and Mannige, Ranjan V and Whitelam, Stephen},
  Journal                  = {Soft matter},
  Year                     = {2014},
  Number                   = {34},
  Pages                    = {6404--6416},
  Volume                   = {10},

  Owner                    = {ranjan},
  Publisher                = {Royal Society of Chemistry},
  Timestamp                = {2015.04.20}
}

@Article{Helenius1977,
  Title                    = {Reconstitution of Semliki forest virus membrane.},
  Author                   = {Helenius, A. and Fries, E. and Kartenbeck, J.},
  Journal                  = {J Cell Biol.},
  Year                     = {1977},
  Number                   = {3},
  Pages                    = {866--880},
  Volume                   = {75},

  File                     = {Helenius1977.pdf:pdfs/Helenius1977.pdf:PDF}
}

@Article{Hendrix2004,
  Title                    = {Hot new virus, deep connections},
  Author                   = {Hendrix,R.W.},
  Journal                  = PNAS,
  Year                     = {2004},
  Number                   = {20},
  Pages                    = {7495-7496},
  Volume                   = {101},

  File                     = {Hendrix2004.pdf:pdfs/Hendrix2004.pdf:PDF}
}

@Article{Henikoff1992,
  Title                    = {Amino acid substitution matrices from protein blocks.},
  Author                   = {S. Henikoff and J. G. Henikoff},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1992},

  Month                    = {Nov},
  Number                   = {22},
  Pages                    = {10915--10919},
  Volume                   = {89},

  Abstract                 = {Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.},
  Institution              = {Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98104.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Animals; Caenorhabditis elegans, genetics; Drosophila, genetics; Lod Score; Mathematics; Molecular Sequence Data; Probability; Proteins, chemistry/genetics; Sequence Homology, Amino Acid; Software},
  Owner                    = {ranjan},
  Pmid                     = {1438297},
  Timestamp                = {2010.09.23}
}

@Article{Henrick2003,
  Title                    = {EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information},
  Author                   = {Henrick,K. and Newman,R. and Tagari,M. and Chagoyen,M.},
  Journal                  = {J Struct Biol.},
  Year                     = {2003},
  Number                   = {1-2},
  Pages                    = {228-237},
  Volume                   = {144},

  File                     = {Henrick2003.pdf:pdfs/Henrick2003.pdf:PDF}
}

@Article{Heo2009,
  Title                    = {Emergence of species in evolutionary ``simulated annealing''.},
  Author                   = {Muyoung Heo and Louis Kang and Eugene I Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2009},

  Month                    = {Feb},
  Number                   = {6},
  Pages                    = {1869--1874},
  Volume                   = {106},

  Abstract                 = {Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question by using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and interactions of proteins encoded in their genomes. Simulating evolution of populations, we found that fitness increases in punctuated steps via epistatic events, leading to formation of stable and functionally interacting proteins. At low mutation rates, species form populations of organisms tightly localized in sequence space, whereas at higher mutation rates, species are lost without an apparent loss of fitness. However, when mutation rate was a selectable trait, the population initially maintained high mutation rate until a high fitness level was reached, after which organisms with low mutation rates are gradually selected, with the population eventually reaching mutation rates comparable with those of modern DNA-based organisms. This study 
shows that the fitness landscape of a biophysically realistic system is extremely complex, with huge number of local peaks rendering adaptation dynamics to be a glass-like process. On a more practical level, our results provide a rationale to experimental observations of the effect of mutation rate on fitness of populations of asexual organisms.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.},
  Keywords                 = {Animals; Computer Simulation; Evolution; Evolution, Molecular; Genetic Speciation; Kinetics; Models, Genetic; Mutation; Population Dynamics; Proteins, chemistry/genetics/metabolism; Reproduction, Asexual; Selection (Genetics)},
  Owner                    = {ranjan},
  Pii                      = {0809852106},
  Pmid                     = {19164759},
  Timestamp                = {2009.12.05}
}

@Article{Heo2011,
  Title                    = {Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions.},
  Author                   = {Muyoung Heo and Sergei Maslov and Eugene Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2011},

  Month                    = {Mar},
  Number                   = {10},
  Pages                    = {4258--4263},
  Volume                   = {108},

  Abstract                 = {How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous nonfunctional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are directly determined from its genome through biophysical properties of protein structures and binding interactions in a crowded cellular environment. The model cell includes three independent prototypical pathways, whose topologies of protein-protein interaction (PPI) subnetworks are different, but whose contributions to the cell fitness are equal. Model cells evolve through genotypic mutations and phenotypic protein copy number variations. We found a strong relationship between evolved physical-chemical properties of protein interactions and their abundances due to a "frustration" effect: Strengthening of functional interactions brings about hydrophobic interfaces, which make proteins prone to promiscuous binding. The balancing act is achieved by 
lowering concentrations of hub proteins while raising solubilities and abundances of functional monomers. On the basis of these principles we generated and analyzed a possible realization of the proteome-wide PPI network in yeast. In this simulation we found that high-throughput affinity capture-mass spectroscopy experiments can detect functional interactions with high fidelity only for high-abundance proteins while missing most interactions for low-abundance proteins.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.},
  Keywords                 = {Mutation; Protein Binding; Proteins, genetics/metabolism},
  Owner                    = {ranjan},
  Pii                      = {1009392108},
  Pmid                     = {21368118},
  Timestamp                = {2011.07.05}
}

@Article{Hershberg2010,
  Title                    = {Evidence that mutation is universally biased towards {AT} in bacteria.},
  Author                   = {Hershberg, Ruth and Petrov, Dmitri A.},
  Journal                  = {PLoS Genet},
  Year                     = {2010},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {e1001115},
  Volume                   = {6},

  Abstract                 = {Mutation is the engine that drives evolution and adaptation forward in that it generates the variation on which natural selection acts. Mutation is a random process that nevertheless occurs according to certain biases. Elucidating mutational biases and the way they vary across species and within genomes is crucial to understanding evolution and adaptation. Here we demonstrate that clonal pathogens that evolve under severely relaxed selection are uniquely suitable for studying mutational biases in bacteria. We estimate mutational patterns using sequence datasets from five such clonal pathogens belonging to four diverse bacterial clades that span most of the range of genomic nucleotide content. We demonstrate that across different types of sites and in all four clades mutation is consistently biased towards AT. This is true even in clades that have high genomic GC content. In all studied cases the mutational bias towards AT is primarily due to the high rate of C/G to T/A 
transitions. These results suggest that bacterial mutational biases are far less variable than previously thought. They further demonstrate that variation in nucleotide content cannot stem entirely from variation in mutational biases and that natural selection and/or a natural selection-like process such as biased gene conversion strongly affect nucleotide content.},
  Institution              = {Department of Biology, Stanford University, Stanford, California, United States of America. ruthersh@stanford.edu},
  Keywords                 = {Bacteria, genetics; Base Composition, genetics; Bias (Epidemiology); Genome, Bacterial, genetics; Intracellular Space, microbiology; Mutation, genetics; Nucleotides, genetics; Phylogeny; Sequence Analysis, DNA},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pmid                     = {20838599},
  Timestamp                = {2012.09.26}
}

@Article{Hide1992,
  Title                    = {Structure and evolution of the lipase superfamily.},
  Author                   = {W. A. Hide and L. Chan and W. H. Li},
  Journal                  = {J Lipid Res},
  Year                     = {1992},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {167--178},
  Volume                   = {33},

  Abstract                 = {The lipase superfamily includes three vertebrate and three invertebrate (dipteran) proteins that show significant amino acid sequence similarity to one another. The vertebrate proteins are lipoprotein lipase (LPL), hepatic lipase (HL), and pancreatic lipase (PL). The dipteran proteins are Drosophila yolk proteins 1, 2, and 3. We review the relationships among these proteins that have been established according to gene structural relatedness and introduce our findings on the phylogenetic relationships, distance relationships, and evolutionary history of the lipase gene superfamily. Drosophila yolk proteins contain a 104 amino acid residue segment that is conserved with respect to the lipases. We have used the yolk proteins as an outgroup to root a phylogeny of the lipase family. Our phylogenetic reconstruction suggests that ancestral PL diverged earlier than HL and LPL, which share a more recent root. Human and bovine LPL are shown to be more closely related to murine LPL than to 
guinea pig LPL. A comparison of the distance (a measure of the number of substitutions between sequences) between mammalian and avian LPL reveals that guinea pig LPL has the largest distance from the other mammals. Human, rodent, and rabbit HL show marked divergence from one another, although they have similar relative rates of amino acid substitution when compared to human LPL as an outgroup. Human and porcine PL are not as divergent as human and rat HL, suggesting that PL is more conserved than HL. However, canine PL demonstrates an unusually rapid rate of substitution with respect to the other pancreatic lipases. The lipases share several structurally conserved features. One highly conserved sequence (Gly-Xaa-Ser-Xaa-Gly) contains the active site serine. This feature, which agrees with that found in serine esterases and proteases, is found within the entire spectrum of lipases, including the evolutionarily unrelated prokaryotic lipases. We review the location and possible activity of putative lipid 
binding domains. We have constructed a conservation index (CI) to display conserved structural features within the lipase gene family, a CI of 1.0 signifying perfect conservation. We have found a correlation between a high CI and the position of conserved functional structures. The putative lipid-binding domains of LPL and HL, the disulfide-bridging cysteine residues, catalytic residues, and N-linked glycosylation sites of LPL, HL, and PL all lie within regions having a CI of 0.8 or higher. A number of amino acid substitutions have been identified in familial hyperchylomicronemia which result in loss of LPL function.(ABSTRACT TRUNCATED AT 400 WORDS)},
  Institution              = {Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030.},
  Keywords                 = {Amino Acid Sequence; Animals; Biological Evolution; Humans; Lipase, chemistry/genetics/metabolism; Molecular Sequence Data; Multigene Family; Sequence Alignment},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {1569370},
  Timestamp                = {2011.09.15}
}

@Article{Higgs2009,
  Title                    = {A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code.},
  Author                   = {Paul G Higgs and Ralph E Pudritz},
  Journal                  = {Astrobiology},
  Year                     = {2009},

  Month                    = {Jun},
  Number                   = {5},
  Pages                    = {483--490},
  Volume                   = {9},

  Abstract                 = {Of the 20 amino acids used in proteins, 10 were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these 10 early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be 
universal.},
  File                     = {Higgs2009.pdf:pdfs/Higgs2009.pdf:PDF},
  Institution              = {Origins Institute and Department of Physics and Astronomy, McMaster University, Ontario, Canada. higgsp@mcmaster.ca},
  Keywords                 = {Amino Acids, analysis/chemical synthesis; Biogenesis; Codon; Evolution, Chemical; Evolution, Molecular; Genetic Code; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {19566427},
  Timestamp                = {2009.10.03}
}

@Article{Hilser2007,
  Title                    = {Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins},
  Author                   = {Hilser, Vincent J and Thompson, E Brad},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2007},
  Number                   = {20},
  Pages                    = {8311--8315},
  Volume                   = {104},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2013.11.21}
}

@Article{Himmelreich1997,
  Title                    = {Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium.},
  Author                   = {R. Himmelreich and H. Plagens and H. Hilbert and B. Reiner and R. Herrmann},
  Journal                  = {Nucleic Acids Res},
  Year                     = {1997},

  Month                    = {Feb},
  Number                   = {4},
  Pages                    = {701--712},
  Volume                   = {25},

  Abstract                 = {The sequenced genomes of the two closely related bacteria Mycoplasma genitalium and Mycoplasma pneumoniae were compared with emphasis on genome organization and coding capacity. All the 470 proposed open reading frames (ORFs) of the smaller M.genitalium genome (580 kb) were contained in the larger genome (816 kb) of M.pneumoniae. There were some discrepancies in annotation, but inspection of the DNA sequences showed that the corresponding DNA was always present in M. pneumoniae. The two genomes could be subdivided into six segments. The order of orthologous genes was well conserved within individual segments but the order of these segments in both bacteria was different. We explain the different organization of the segments by translocation via homologous recombination. The translocations did not disturb the continuous bidirectional course of transcription in both genomes, starting at the proposed origin of replication. The additional 236 kb in M.pneumoniae,compared with theM.
genitalium genome, were coding for 209 proposed ORFs not identified in M.genitalium. Of these ORFs, 110 were specific to M.pneumoniae exhibiting no significant similarity to M.genitalium ORFs, while 76 ORFs were amplifications of ORFs existing mainly as single copies in M. genitalium. In addition, 23 ORFs containing a copy of either one of the three repetitive DNA sequences RepMP2/3, RepMP4 and RepMP5 were annotated in M.pneumoniae but not in M.genitalium,although similar DNA sequences were present. TheM.pneumoniae-specific genes included a restriction-modification system, two transport systems for carbohydrates, the complete set of three genes coding for the arginine dihydrolase pathway and 14 copies of the repetitive DNA sequence RepMP1 which were part of several different translated genes with unknown function.},
  File                     = {Himmelreich1997.pdf:pdfs/Himmelreich1997.pdf:PDF},
  Institution              = {Zentrum f?r Molekulare Biologie Heidelberg, Universit?t Heidelberg, Germany.},
  Keywords                 = {Base Composition; Chromosome Mapping; Codon, chemistry/physiology; Genes, Bacterial; Genome, Bacterial; Mycoplasma pneumoniae, chemistry/cytology/genetics; Mycoplasma, chemistry/cytology/genetics; Open Reading Frames, physiology; Sequence Homology, Nucleic Acid},
  Owner                    = {ranjan},
  Pii                      = {gka168},
  Pmid                     = {9016618},
  Timestamp                = {2010.05.20}
}

@Book{Hinchliffe2002,
  Title                    = {Molecular Modelling for Beginners},
  Author                   = {Alan Hinchliffe},
  Publisher                = {Wiley},
  Year                     = {2002},
  Edition                  = {2},

  Owner                    = {ranjan},
  Timestamp                = {2012.07.14}
}

@Article{Ho2005,
  Title                    = {The Ramachandran plots of glycine and pre-proline},
  Author                   = {Ho, Bosco K and Brasseur, Robert},
  Journal                  = {BMC structural biology},
  Year                     = {2005},
  Number                   = {1},
  Pages                    = {1},
  Volume                   = {5},

  Owner                    = {ranjan},
  Publisher                = {BioMed Central},
  Timestamp                = {2016.06.03}
}

@Article{Hooft1997,
  Title                    = {Objectively judging the quality of a protein structure from a Ramachandran plot},
  Author                   = {Hooft, Rob WW and Sander, Chris and Vriend, Gerrit},
  Journal                  = {Computer applications in the biosciences: CABIOS},
  Year                     = {1997},
  Number                   = {4},
  Pages                    = {425--430},
  Volume                   = {13},

  Owner                    = {ranjan},
  Publisher                = {Oxford Univ Press},
  Timestamp                = {2015.09.17}
}

@Article{Hoover1985,
  Title                    = {Canonical dynamics: Equilibrium phase-space distributions.},
  Author                   = {Hoover},
  Journal                  = {Phys Rev A},
  Year                     = {1985},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {1695--1697},
  Volume                   = {31},

  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9895674},
  Timestamp                = {2014.05.12}
}

@Article{Horibe2011,
  Title                    = {Mode Switching and Collective Behavior in Chemical Oil Droplets.},
  Author                   = {Naoto Horibe and Martin Hanczyc and Takashi Ikegami},
  Journal                  = {Entropy},
  Year                     = {2011},
  Pages                    = {709-719},
  Volume                   = {13},

  Owner                    = {ranjan},
  Timestamp                = {2011.05.13}
}

@Article{Horne1961,
  Title                    = {Symmetry in virus architecture},
  Author                   = {Horne, R.W. and Wildy, P.},
  Journal                  = {Virology.},
  Year                     = {1961},
  Number                   = {15},
  Pages                    = {348-373},
  Volume                   = {28},

  File                     = {Horne1961.pdf:pdfs/Horne1961.pdf:PDF}
}

@Article{Hou2008,
  Title                    = {Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain.},
  Author                   = {Tingjun Hou and Wei Zhang and David A Case and Wei Wang},
  Journal                  = {J Mol Biol},
  Year                     = {2008},

  Month                    = {Feb},
  Number                   = {4},
  Pages                    = {1201--1214},
  Volume                   = {376},

  Abstract                 = {Many important protein-protein interactions are mediated by peptide recognition modular domains, such as the Src homology 3 (SH3), SH2, PDZ, and WW domains. Characterizing the interaction interface of domain-peptide complexes and predicting binding specificity for modular domains are critical for deciphering protein-protein interaction networks. Here, we propose the use of an energetic decomposition analysis to characterize domain-peptide interactions and the molecular interaction energy components (MIECs), including van der Waals, electrostatic, and desolvation energy between residue pairs on the binding interface. We show a proof-of-concept study on the amphiphysin-1 SH3 domain interacting with its peptide ligands. The structures of the human amphiphysin-1 SH3 domain complexed with 884 peptides were first modeled using virtual mutagenesis and optimized by molecular mechanics (MM) minimization. Next, the MIECs between domain and peptide residues were computed using the MM/
generalized Born decomposition analysis. We conducted two types of statistical analyses on the MIECs to demonstrate their usefulness for predicting binding affinities of peptides and for classifying peptides into binder and non-binder categories. First, combining partial least squares analysis and genetic algorithm, we fitted linear regression models between the MIECs and the peptide binding affinities on the training data set. These models were then used to predict binding affinities for peptides in the test data set; the predicted values have a correlation coefficient of 0.81 and an unsigned mean error of 0.39 compared with the experimentally measured ones. The partial least squares-genetic algorithm analysis on the MIECs revealed the critical interactions for the binding specificity of the amphiphysin-1 SH3 domain. Next, a support vector machine (SVM) was employed to build classification models based on the MIECs of peptides in the training set. A rigorous training-validation procedure was used to assess 
the performances of different kernel functions in SVM and different combinations of the MIECs. The best SVM classifier gave satisfactory predictions for the test set, indicated by average prediction accuracy rates of 78\% and 91\% for the binding and non-binding peptides, respectively. We also showed that the performance of our approach on both binding affinity prediction and binder/non-binder classification was superior to the performances of the conventional MM/Poisson-Boltzmann solvent-accessible surface area and MM/generalized Born solvent-accessible surface area calculations. Our study demonstrates that the analysis of the MIECs between peptides and the SH3 domain can successfully characterize the binding interface, and it provides a framework to derive integrated prediction models for different domain-peptide systems.},
  Institution              = {Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA.},
  Keywords                 = {Amino Acid Sequence; Humans; Least-Squares Analysis; Models, Molecular; Molecular Sequence Data; Nerve Tissue Proteins, chemistry/metabolism; Peptides, metabolism; Principal Component Analysis; Protein Binding; Thermodynamics; src Homology Domains},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(07)01685-3},
  Pmid                     = {18206907},
  Timestamp                = {2009.06.21}
}

@Article{Hovmoeller2002,
  Title                    = {Conformations of amino acids in proteins},
  Author                   = {Hovm{\"o}ller, Sven and Zhou, Tuping and Ohlson, Tomas},
  Journal                  = {Acta Crystallographica Section D: Biological Crystallography},
  Year                     = {2002},
  Number                   = {5},
  Pages                    = {768--776},
  Volume                   = {58},

  Owner                    = {ranjan},
  Publisher                = {International Union of Crystallography},
  Timestamp                = {2015.09.17}
}

@Article{Huang2009,
  Title                    = {Kinetic advantage of intrinsically disordered proteins in coupled folding--binding process: a critical assessment of the `fly-casting' mechanism},
  Author                   = {Huang, Yongqi and Liu, Zhirong},
  Journal                  = {Journal of molecular biology},
  Year                     = {2009},
  Number                   = {5},
  Pages                    = {1143--1159},
  Volume                   = {393},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.21}
}

@Article{Hubner2004,
  Title                    = {Simulation, experiment, and evolution: understanding nucleation in protein S6 folding.},
  Author                   = {Isaac A Hubner and Mikael Oliveberg and Eugene I Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2004},

  Month                    = {Jun},
  Number                   = {22},
  Pages                    = {8354--8359},
  Volume                   = {101},

  Abstract                 = {In this study, we explore nucleation and the transition state ensemble of the ribosomal protein S6 using a Monte Carlo (MC) Go model in conjunction with restraints from experiment. The results are analyzed in the context of extensive experimental and evolutionary data. The roles of individual residues in the folding nucleus are identified, and the order of events in the S6 folding mechanism is explored in detail. Interpretation of our results agrees with, and extends the utility of, experiments that shift phi-values by modulating denaturant concentration and presents strong evidence for the realism of the mechanistic details in our MC Go model and the structural interpretation of experimental phi-values. We also observe plasticity in the contacts of the hydrophobic core that support the specific nucleus. For S6, which binds to RNA and protein after folding, this plasticity may result from the conformational flexibility required to achieve biological function. These results 
present a theoretical and conceptual picture that is relevant in understanding the mechanism of nucleation in protein folding.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.},
  Keywords                 = {Bacterial Proteins, chemistry; Evolution, Molecular; Models, Molecular; Monte Carlo Method; Protein Conformation; Protein Folding; Ribosomal Protein S6, chemistry; Thermus thermophilus},
  Owner                    = {ranjan},
  Pii                      = {0401672101},
  Pmid                     = {15150413},
  Timestamp                = {2009.12.05}
}

@Article{Hughes1999a,
  Title                    = {Evolution of the arthropod prophenoloxidase/hexamerin protein family.},
  Author                   = {A. L. Hughes},
  Journal                  = {Immunogenetics},
  Year                     = {1999},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {106--114},
  Volume                   = {49},

  Abstract                 = {Phylogenetic analysis of the prophenoloxidase/hexamerin family of arthropods revealed four well supported subfamilies: (1) the arylphorin subfamily, including arylphorins, storage proteins, and other proteins of uncertain function from insects; (2) the hemocyanins of branchiopod crustaceans, which are copper-binding proteins involved in oxygen transport; (3) the hemocyanins of chelicerates; and (4) the prophenoloxidases (proPO) of both insects and branchiopods, which are copper-binding molecules that play a role in sclerotization of cuticle and encapsulation of foreign particles. The phylogeny indicated that insect and branchiopod proPO constitute a monophyletic group but that branchiopod and chelicerate hemocyanins do not constitute a monophyletic group. Branchiopod hemocyanin and proPO diverged from each other prior to the divergence of insects from branchiopods and probably prior to the divergence of chelicerates from the insect-branchiopod lineage. Likewise, the insect 
arylphorin subfamily diverged from proPO prior to the divergence of insects from branchiopods and probably prior to the divergence of chelicerates; thus, the results did not support the hypothesis that insect arylphorins represent hemocyanins freed to assume a new function because the insect tracheal respiratory system removes the need for an oxygen-transport molecule. Nonetheless, reconstruction of ancestral sequences by the maximum parsimony method suggested that the ancestors of the arylphorin family were copper-binding. Regions corresponding to the copper-binding domains were found to have a faster rate of nonsynonymous evolution in arylphorin subfamily genes than in other hexamerin family genes; this presumably reflects a relaxation of purifying selection after the loss of copper-binding function.},
  Institution              = {Department of Biology, Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park 16803, USA. austin@hugans3.bio.psu.edu},
  Keywords                 = {Amino Acid Sequence; Animals; Arthropods, enzymology/genetics; Catechol Oxidase, chemistry/genetics; Enzyme Precursors, chemistry/genetics; Evolution, Molecular; Glycoproteins, chemistry/genetics; Hemocyanin, chemistry/genetics; Insect Proteins, chemistry/genetics; Molecular Sequence Data; Multigene Family; Phylogeny; Probability; Sequence Alignment; Sequence Homology, Amino Acid},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9887347},
  Timestamp                = {2011.09.15}
}

@Article{Hughes1994,
  Title                    = {The evolution of functionally novel proteins after gene duplication},
  Author                   = {Hughes, Austin L},
  Journal                  = {Proceedings of the Royal Society of London. Series B: Biological Sciences},
  Year                     = {1994},
  Number                   = {1346},
  Pages                    = {119--124},
  Volume                   = {256},

  Owner                    = {ranjan},
  Publisher                = {The Royal Society},
  Timestamp                = {2013.11.30}
}

@Article{Hughes1999,
  Title                    = {Coevolution of the mammalian chemokines and their receptors.},
  Author                   = {A. L. Hughes and M. Yeager},
  Journal                  = {Immunogenetics},
  Year                     = {1999},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {115--124},
  Volume                   = {49},

  Abstract                 = {A phylogeny of mammalian chemokines revealed two major clusters, corresponding to the CC and CXC chemokines; the C chemokines appeared to be more closely related to the former. In a phylogeny of chemokine receptors, there were also two major clusters: one containing CC chemokine receptors plus other receptors of unknown function and another containing CXC receptors and other receptors of unknown function. However, within the CC receptors, there was not a close correspondence between the phylogenies of chemokines and their receptors. The CC chemokines contained two major subfamilies: (1) the MIP subfamily (including MIP-1alpha, MIP-1beta, and RANTES); and (2) the MCP subfamily (including MCP-1,-2,-3, and -4 and eotaxin). Receptors having preferred ligands in the MCP subfamily did not constitute a monophyletic group but rather evolved twice independently. Reconstruction of ancestral amino acid sequences suggested that these two groups of MCP receptors did not convergently evolve 
any amino acid residues; rather, they convergently lost sequence features found in the third and fourth extracellular domains of known receptors for MIP-subfamily chemokines.},
  Institution              = {Department of Biology, Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park 16802, USA.},
  Keywords                 = {Amino Acid Sequence; Animals; Artiodactyla; Cats; Cattle; Chemokines, CC, metabolism; Chemokines, chemistry/genetics; Evolution, Molecular; Guinea Pigs; Humans; Mice; Molecular Sequence Data; Multigene Family; Phylogeny; Primates; Rabbits; Rats; Receptors, Chemokine, chemistry/genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9887348},
  Timestamp                = {2011.09.15}
}

@Article{Huguet1997,
  Title                    = {Rel/NF-kappa B transcription factors and I kappa B inhibitors: evolution from a unique common ancestor.},
  Author                   = {C. Huguet and P. Crepieux and V. Laudet},
  Journal                  = {Oncogene},
  Year                     = {1997},

  Month                    = {Dec},
  Number                   = {24},
  Pages                    = {2965--2974},
  Volume                   = {15},

  Abstract                 = {From the sequences of Rel/NF-kappa B and I kappa B proteins, we constructed an alignment of their Rel Homology Domain (RHD) and ankyrin repeat domain. Using this alignment, we performed tree reconstruction with both distance matrix and parsimony analysis and estimated the branching robustness using bootstrap resampling methods. We defined four subfamilies of Rel/NF-kappa B transcription factors: (i) cRel, RelA, RelB, Dorsal and Dif; (ii) NF-kappa B1 and NF-kappa B2; (iii) Relish and (iv) NF-AT factors, the most divergent members. Subfamilies I and II are clustered together whereas Relish diverged earlier than other Rel/NF-kappa B proteins. Three subfamilies of I kappa B inhibitors were also defined: (i) NF-kappa B1 and NF-kappa B2; (ii) close to subfamily I, the short I kappa B proteins I kappa B alpha, I kappa B beta and Bcl-3; (iii) Relish that diverged earlier than other I kappa B inhibitors. Our definition of groups and subfamilies fits to structural and functional features 
of the Rel/NF-kappa B and I kappa B proteins. We also showed that ankyrin repeats of NF-kappa B1, NF-kappa B2 and Relish are short I kappa B-specific ankyrin motifs. These proteins defining a link between Rel/NF-kappa B and I kappa B families, we propose that all these factors evolved from a common ancestral RHD-ankyrin structure within a unique superfamily, explaining the specificities of interaction between the different Rel/NF-kappa B dimers and the various I kappa B inhibitors.},
  Institution              = {Laboratoire de r?gulation des processus invasifs, de l'angiogen?se et de l'apoptose, EP560, IFR3 Institut de Biologie de Lille, France.},
  Keywords                 = {Amino Acid Sequence; Animals; Chickens; Drosophila; Evolution, Molecular; Humans; Mice; Multigene Family; NF-kappa B, analysis/genetics; Phylogeny; Proto-Oncogene Proteins c-rel; Proto-Oncogene Proteins, analysis/antagonists /&/ inhibitors/genetics; Rats; Sequence Alignment; Swine; Transcription Factor RelB; Transcription Factors; Turkeys; Xenopus; Xenopus Proteins},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9416840},
  Timestamp                = {2011.09.15}
}

@Article{Huiskonen2009,
  Title                    = {Electron cryo-microscopy and single-particle averaging of Rift Valley fever virus: evidence for GN-GC glycoprotein heterodimers.},
  Author                   = {Juha T Huiskonen and Anna K Overby and Friedemann Weber and Kay Gr\"unewald},
  Journal                  = {J Virol},
  Year                     = {2009},

  Month                    = {Apr},
  Number                   = {8},
  Pages                    = {3762--3769},
  Volume                   = {83},

  Abstract                 = {Rift Valley fever virus (RVFV) is a member of the genus Phlebovirus within the family Bunyaviridae. It is a mosquito-borne zoonotic agent that can cause hemorrhagic fever in humans. The enveloped RVFV virions are known to be covered by capsomers of the glycoproteins G(N) and G(C), organized on a T=12 icosahedral lattice. However, the structural units forming the RVFV capsomers have not been determined. Conflicting biochemical results for another phlebovirus (Uukuniemi virus) have indicated the existence of either G(N) and G(C) homodimers or G(N)-G(C) heterodimers in virions. Here, we have studied the structure of RVFV using electron cryo-microscopy combined with three-dimensional reconstruction and single-particle averaging. The reconstruction at 2.2-nm resolution revealed the organization of the glycoprotein shell, the lipid bilayer, and a layer of ribonucleoprotein (RNP). Five- and six-coordinated capsomers are formed by the same basic structural unit. Molecular-mass 
measurements suggest a G(N)-G(C) heterodimer as the most likely candidate for this structural unit. Both leaflets of the lipid bilayer were discernible, and the glycoprotein transmembrane densities were seen to modulate the curvature of the lipid bilayer. RNP densities were situated directly underneath the transmembrane densities, suggesting an interaction between the glycoprotein cytoplasmic tails and the RNPs. The success of the single-particle averaging approach taken in this study suggests that it is applicable in the study of other phleboviruses, as well, enabling higher-resolution description of these medically important pathogens.},
  Institution              = {Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany. huiskone@biochem.mpg.de},
  Keywords                 = {Cryoelectron Microscopy; Dimerization; Imaging, Three-Dimensional; Rift Valley fever virus, ultrastructure; Viral Envelope Proteins, metabolism/ultrastructure},
  Owner                    = {ranjan},
  Pii                      = {JVI.02483-08},
  Pmid                     = {19193794},
  Timestamp                = {2010.01.22}
}

@Article{Hung1998,
  Title                    = {Structure of an enantiomeric protein, d-monellin at 1.8 {\AA} resolution},
  Author                   = {Hung, Li-Wei and Kohmura, Masanori and Ariyoshi, Y and Kim, S-H},
  Journal                  = {Acta Crystallographica Section D: Biological Crystallography},
  Year                     = {1998},
  Number                   = {4},
  Pages                    = {494--500},
  Volume                   = {54},

  Owner                    = {ranjan},
  Publisher                = {International Union of Crystallography},
  Timestamp                = {2016.06.06}
}

@Article{Hurst2006,
  Title                    = {Protein evolution: causes of trends in amino-acid gain and loss.},
  Author                   = {Laurence D Hurst and Edward J Feil and Eduardo P C Rocha},
  Journal                  = {Nature},
  Year                     = {2006},

  Month                    = {Aug},
  Number                   = {7105},
  Pages                    = {E11--2; discussion E12},
  Volume                   = {442},

  Abstract                 = {Understanding how proteins evolve is important for determining the molecular basis of adaptation, for inferring phylogenies and for engineering novel proteins. It has been suggested that some amino acids were incorporated into the genetic code more recently than others and, after comparing pairs of closely related genomes, Jordan et al. report that 'recent' amino acids are becoming more common. They argue that this process has been going on since the genetic code first evolved to encompass all 20 amino acids. Here we provide evidence that the patterns observed conform with standard, nearly neutral theoretical expectations and require no new explanation. This reinforces the need for caution in the interpretation of results derived from closely related taxa.},
  Institution              = {Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK. hurst@bath.ac.uk},
  Keywords                 = {Amino Acids, genetics/metabolism; Animals; Bacillus, genetics; Bacterial Proteins, chemistry/genetics; Escherichia coli, genetics; Evolution, Molecular; Genetic Code; Genome, Bacterial; Humans; Models, Genetic; Mutation, genetics; Polymorphism, Genetic, genetics; Proteins, chemistry/genetics; Staphylococcus, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nature05137},
  Pmid                     = {16929253},
  Timestamp                = {2011.09.15}
}

@Article{Iakoucheva2002,
  Title                    = {Intrinsic disorder in cell-signaling and cancer-associated proteins},
  Author                   = {Iakoucheva, Lilia M and Brown, Celeste J and Lawson, J David and Obradovi{\'c}, Zoran and Dunker, A Keith},
  Journal                  = {Journal of molecular biology},
  Year                     = {2002},
  Number                   = {3},
  Pages                    = {573--584},
  Volume                   = {323},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.19}
}

@Article{Innan1997,
  Title                    = {The amounts of nucleotide variation within and between allelic classes and the reconstruction of the common ancestral sequence in a population.},
  Author                   = {H. Innan and F. Tajima},
  Journal                  = {Genetics},
  Year                     = {1997},

  Month                    = {Nov},
  Number                   = {3},
  Pages                    = {1431--1444},
  Volume                   = {147},

  Abstract                 = {The amounts of nucleotide variation within and between allelic classes were studied. The expectation and variance of the number of segregating sites and the expectation of the average number of pairwise differences among a sample of DNA sequences were obtained by using the theory of gene genealogy with no recombination. When the ancestral allelic class is unknown, it was found that the amount of variation within an allelic class increases with its frequency in the sample, while the amount of variation between two allelic classes is the largest when the two allelic classes exist equally. On the other hand, if we know the ancestral allelic class, as the frequency of the mutant allelic class increases, the amounts of variation within the mutant allelic class and between two allelic classes increase and the amount of variation within the ancestral allelic class decreases. As an example, we analyzed the polymorphism in the ND5 gene of Drosophila melanogaster and constructed the 
common ancestral sequence with high confidence, suggesting that the pattern of polymorphism within species gives useful information to know the ancestral sequence of the species.},
  Institution              = {Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan.},
  Keywords                 = {Alleles; Animals; Drosophila melanogaster, enzymology/genetics; Genetic Variation; Insect Proteins, genetics; Mathematical Computing; Models, Genetic; NADH Dehydrogenase, genetics; Nucleotides; Population},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9383083},
  Timestamp                = {2011.09.15}
}

@Article{Irbaeck2000,
  Title                    = {On hydrophobicity correlations in protein chains.},
  Author                   = {A. Irb?ck and E. Sandelin},
  Journal                  = {Biophys J},
  Year                     = {2000},

  Month                    = {Nov},
  Number                   = {5},
  Pages                    = {2252--2258},
  Volume                   = {79},

  Abstract                 = {We study the statistical properties of hydrophobic/polar model sequences with unique native states on the square lattice. It is shown that this ensemble of sequences differs from random sequences in significant ways in terms of both the distribution of hydrophobicity along the chains and total hydrophobicity. Whenever statistically feasible, the analogous calculations are performed for a set of real enzymes, too.},
  Institution              = {Complex Systems Division, Department of Theoretical Physics, Lund University, S?lvegatan 14A, S-223 62 Lund, Sweden. irback@thep.lu.se},
  Keywords                 = {Biophysical Phenomena; Biophysics; Enzymes, chemistry; Models, Chemical; Protein Folding; Proteins, chemistry},
  Owner                    = {ranjan},
  Pii                      = {S0006-3495(00)76472-1},
  Pmid                     = {11053106},
  Timestamp                = {2010.09.22}
}

@Article{Itan2009,
  Title                    = {The origins of lactase persistence in Europe.},
  Author                   = {Yuval Itan and Adam Powell and Mark A Beaumont and Joachim Burger and Mark G Thomas},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2009},

  Month                    = {Aug},
  Number                   = {8},
  Pages                    = {e1000491},
  Volume                   = {5},

  Abstract                 = {Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (-13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the--13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model where lactase persistence is only favoured in cultures practicing dairying, and dairying is more favoured in lactase persistent populations. We have developed a flexible demic computer simulation model to explore the spread of lactase persistence, dairying, other subsistence practices and 
unlinked genetic markers in Europe and western Asia's geographic space. Using data on--13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the--13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D. Our results provide a coherent and spatially explicit picture of the coevolution of lactase persistence and dairying in Europe.},
  Institution              = {Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.},
  Owner                    = {ranjan},
  Pmid                     = {19714206},
  Timestamp                = {2009.10.11}
}

@Article{Ivanyi-Nagy2010,
  Title                    = {Intrinsic disorder in the core proteins of flaviviruses},
  Author                   = {Ivanyi-Nagy, Roland and Darlix, Jean-Luc},
  Journal                  = {Protein and Peptide Letters},
  Year                     = {2010},
  Number                   = {8},
  Pages                    = {1019--1025},
  Volume                   = {17},

  Owner                    = {ranjan},
  Publisher                = {Bentham Science Publishers},
  Timestamp                = {2013.12.06}
}

@Article{Lee2016,
  Title                    = {CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field},
  Author                   = {Lee J. and Cheng X. and Swails J.M. and Yeom M.S. and Eastman P.K. and Lemkul J.A. and Wei S. and Buckner J. and Jeong J.C. and Qi Y. and Jo S. Pande V.S. and Case D.A. and Brooks C.L~3rd and MacKerell A.D~Jr and Klauda J.B. and Im W.},
  Journal                  = {J Chem Theory Comput.},
  Year                     = {2016},
  Number                   = {1},
  Pages                    = {405-413},
  Volume                   = {12},

  Owner                    = {ranjan},
  Timestamp                = {2016.08.28}
}

@Article{Jaalinoja2008,
  Title                    = {Structure and host-cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus},
  Author                   = {J\"a\"alinoja, H.T and Roine, E. and Laurinm\"aki, P. and Kivel\"a, H.M. and Bamford, D.H. and Butcher, S.J.},
  Journal                  = PNAS,
  Year                     = {2008},
  Number                   = {23},
  Pages                    = {8008--8013},
  Volume                   = {105},

  File                     = {Jaalinoja2008.pdf:pdfs/Jaalinoja2008.pdf:PDF}
}

@Article{Jacob1977,
  Title                    = {Evolution and tinkering},
  Author                   = {F Jacob},
  Journal                  = {Science},
  Year                     = {1977},
  Number                   = {4295},
  Pages                    = {1161},
  Volume                   = {196},

  Owner                    = {ranjan},
  Timestamp                = {2010.09.02}
}

@Article{Jacrot1975,
  Title                    = {Studies on the assembly of a spherical plant virus. II. The mechanism of protein aggregation and virus swelling.},
  Author                   = {Jacrot, B.},
  Journal                  = JMB,
  Year                     = {1975},
  Number                   = {3},
  Pages                    = {433--446},
  Volume                   = {95},

  File                     = {Jacrot1975.pdf:pdfs/Jacrot1975.pdf:PDF}
}

@Article{Jain2005,
  Title                    = {Evolutionary trajectories in rugged fitness landscapes},
  Author                   = {Kavita Jain and Joachim Krug},
  Journal                  = {J. Stat. Mech.},
  Year                     = {2005},
  Pages                    = {P04008},

  Owner                    = {ranjan},
  Timestamp                = {2011.11.22}
}

@Article{James2003b,
  Title                    = {Antibody multispecificity mediated by conformational diversity.},
  Author                   = {Leo C James and Pietro Roversi and Dan S Tawfik},
  Journal                  = {Science},
  Year                     = {2003},

  Month                    = {Feb},
  Number                   = {5611},
  Pages                    = {1362--1367},
  Volume                   = {299},

  Abstract                 = {A single antibody was shown to adopt different binding-site conformations and thereby bind unrelated antigens. Analysis by both x-ray crystallography and pre-steady-state kinetics revealed an equilibrium between different preexisting isomers, one of which possessed a promiscuous, low-affinity binding site for aromatic ligands, including the immunizing hapten. A subsequent induced-fit isomerization led to high-affinity complexes with a deep and narrow binding site. A protein antigen identified by repertoire selection made use of an unrelated antibody isomer with a wide, shallow binding site. Conformational diversity, whereby one sequence adopts multiple structures and multiple functions, can increase the effective size of the antibody repertoire but may also lead to autoimmunity and allergy.},
  Institution              = {Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2HQ, UK.},
  Keywords                 = {2,4-Dinitrophenol, immunology; Amino Acid Sequence; Antibodies, Monoclonal, chemistry/immunology; Antibody Diversity; Antibody Specificity; Antigen-Antibody Complex; Antigen-Antibody Reactions; Antigens, immunology; Binding Sites, Antibody; Cross Reactions; Crystallization; Crystallography, X-Ray; Dimerization; Haptens, immunology; Hydrogen Bonding; Immunoglobulin E, chemistry/immunology; Immunoglobulin Fragments, chemistry/immunology; Isomerism; Kinetics; Ligands; Models, Molecular; Molecular Sequence Data; Peptide Library; Protein Conformation; Recombinant Proteins, immunology},
  Owner                    = {ranjan},
  Pii                      = {299/5611/1362},
  Pmid                     = {12610298},
  Timestamp                = {2010.04.30}
}

@Article{James2003,
  Title                    = {The specificity of cross-reactivity: promiscuous antibody binding involves specific hydrogen bonds rather than nonspecific hydrophobic stickiness.},
  Author                   = {Leo C James and Dan S Tawfik},
  Journal                  = {Protein Sci},
  Year                     = {2003},

  Month                    = {Oct},
  Number                   = {10},
  Pages                    = {2183--2193},
  Volume                   = {12},

  Abstract                 = {Proteins are renowned for their specificity of function. There is, however, accumulating evidence that many proteins, from enzymes to antibodies, are functionally promiscuous. Promiscuity is of considerable physiological importance. In the immune system, cross-reactive or multispecific antibodies are implicated in autoimmune and allergy conditions. In most cases, however, the mechanism behind promiscuity and the relationship between specific and promiscuous activities are unknown. Are the two contradictory? Or can a protein exhibit several unrelated activities each of which is highly specific? To address these questions, we studied a multispecific IgE antibody (SPE7) elicited against a 2,4-dinitrophenyl hapten (DNP). SPE7 is able to distinguish between closely related derivatives such as NP (nitrophenol) and DNP, yet it can also bind a number of unrelated ligands. We find that, like DNP, the cross-reactants are themselves bound specifically-close derivatives of these cross-
reactants show very low or no binding to SPE7. It has been suggested that cross-reactivity is simply due to "hydrophobic stickiness", nonspecific interactions between hydrophobic ligands and binding sites. However, partitioning experiments reveal that affinity for SPE7 is unrelated to ligand hydrophobicity. These data, combined with crystal structures of SPE7 in complex with four different ligands, demonstrate that each cross-reactant is bound specifically, forming different hydrogen bonds dependant upon its particular chemistry and the availability of complementary antibody residues. SPE7 is highly homologous to the germline antinitrophenol (NP) antibody B1-8. By comparing the sequences and binding patterns of SPE7 and B1-8, we address the relationship between affinity maturation, specificity, and cross-reactivity.},
  Institution              = {MRC Laboratory of Molecular Biology, Cambridge CB2 2HQ, United Kingdom.},
  Keywords                 = {Amino Acid Sequence; Animals; Anthracenes, chemistry; Anthraquinones, chemistry/immunology; Antibody Affinity, immunology; Antibody Specificity, immunology; Base Sequence; Binding, Competitive, immunology; Cloning, Molecular; Cross Reactions, immunology; Crystallography, X-Ray; Dinitrophenols, chemistry/immunology; Enzyme-Linked Immunosorbent Assay, methods; Haptens, chemistry/immunology; Hydrogen Bonding; Hydrophobicity; Immunoglobulin E, chemistry/immunology; Immunoglobulin Fab Fragments, genetics/immunology; Immunoglobulin Variable Region, genetics/immunology; Mice; Models, Molecular; Molecular Sequence Data; Molecular Structure; Nitrophenols, chemistry/immunology; Recombinant Proteins, genetics/immunology; Schiff Bases, chemistry; Sequence Analysis, DNA; Sequence Homology, Amino Acid},
  Owner                    = {ranjan},
  Pmid                     = {14500876},
  Timestamp                = {2010.04.30}
}

@Article{James2003a,
  Title                    = {Conformational diversity and protein evolution--a 60-year-old hypothesis revisited.},
  Author                   = {Leo C James and Dan S Tawfik},
  Journal                  = {Trends Biochem Sci},
  Year                     = {2003},

  Month                    = {Jul},
  Number                   = {7},
  Pages                    = {361--368},
  Volume                   = {28},

  Institution              = {Centre for Protein Engineering, Hills Road, Cambridge, UK CB2 2HQ.},
  Keywords                 = {Animals; Evolution, Molecular; Humans; Protein Conformation; Proteins, chemistry/genetics},
  Owner                    = {ranjan},
  Pii                      = {S096800040300135X},
  Pmid                     = {12878003},
  Timestamp                = {2010.04.30}
}

@Article{Janin1983,
  Title                    = {Structural domains in proteins and their role in the dynamics of protein function},
  Author                   = {Janin, Jo{\"e}l and Wodak, Shoshanna J},
  Journal                  = {Progress in biophysics and molecular biology},
  Year                     = {1983},
  Pages                    = {21--78},
  Volume                   = {42},

  Owner                    = {ranjan},
  Publisher                = {Pergamon},
  Timestamp                = {2013.08.15}
}

@Article{Javidpour2011,
  Title                    = {Confinement in nanopores can destabilize Alpha-helix folding proteins and stabilize the Beta structures.},
  Author                   = {Leili Javidpour and Muhammad Sahimi},
  Journal                  = {J Chem Phys},
  Year                     = {2011},

  Month                    = {Sep},
  Number                   = {12},
  Pages                    = {125101},
  Volume                   = {135},

  Abstract                 = {Protein folding in confined media has attracted wide attention over the past decade due to its importance in both in vivo and in vitro applications. Currently, it is generally believed that protein stability increases by decreasing the size of the confining medium, if its interaction with the confining walls is repulsive, and that the maximum folding temperature in confinement occurs for a pore size only slightly larger than the smallest dimension of the folded state of a protein. Protein stability in pore sizes, very close to the size of the folded state, has not however received the attention that it deserves. Using detailed, 0.3-ms-long molecular dynamics simulations, we show that proteins with an Alpha-helix native state can have an optimal folding temperature in pore sizes that do not affect the folded-state structure. In contradiction to the current theoretical explanations, we find that the maximum folding temperature occurs in larger pores for smaller \Alpha-helices. In 
highly confined pores the free energy surface becomes rough, and a new barrier for protein folding may appear close to the unfolded state. In addition, in small nanopores the protein states that contain the Beta structures are entropically stabilized, in contrast to the bulk. As a consequence, folding rates decrease notably and the free energy surface becomes rougher. The results shed light on many recent experimental observations that cannot be explained by the current theories, and demonstrate the importance of entropic effects on proteins' misfolded states in highly confined environments. They also support the concept of passive effect of chaperonin GroEL on protein folding by preventing it from aggregation in crowded environment of biological cells, and provide deeper clues to the Alpha to Beta conformational transition, believed to contribute to Alzheimer's and Parkinson's diseases. The strategy of protein and enzyme stabilization in confined media may also have to be revisited in the case of tight 
confinement. For in silico studies of protein folding in confined media, use of non-Go potentials may be more appropriate.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Javidpour2011.pdf:PDF},
  Institution              = {School of Physics, Institute for Research in Fundamental Sciences, IPM, Tehran 19395-5531, Iran.},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {21974560},
  Timestamp                = {2011.11.27}
}

@InProceedings{Jaynes1967,
  Title                    = {Foundations of probability theory and statistical mechanics},
  Author                   = {Jaynes, Edwin T},
  Booktitle                = {Delaware Seminar in the Foundations of Physics},
  Year                     = {1967},
  Organization             = {Springer},
  Pages                    = {77--101},

  Owner                    = {ranjan},
  Timestamp                = {2014.11.02}
}

@Article{Jaynes1957,
  Title                    = {Information theory and statistical mechanics},
  Author                   = {Jaynes, Edwin T},
  Journal                  = {Physical review},
  Year                     = {1957},
  Number                   = {4},
  Pages                    = {620},
  Volume                   = {106},

  Owner                    = {ranjan},
  Publisher                = {APS},
  Timestamp                = {2014.11.01}
}

@Article{Jaynes1957a,
  Title                    = {Information theory and statistical mechanics. II},
  Author                   = {Jaynes, Edwin T},
  Journal                  = {Physical review},
  Year                     = {1957},
  Number                   = {2},
  Pages                    = {171},
  Volume                   = {108},

  Owner                    = {ranjan},
  Publisher                = {APS},
  Timestamp                = {2014.11.01}
}

@Article{Jensen2013,
  Title                    = {Describing intrinsically disordered proteins at atomic resolution by NMR},
  Author                   = {Jensen, Malene Ringkj{\o}bing and Ruigrok, Rob WH and Blackledge, Martin},
  Journal                  = {Current opinion in structural biology},
  Year                     = {2013},
  Number                   = {3},
  Pages                    = {426--435},
  Volume                   = {23},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2015.09.17}
}

@Article{Jensen1976,
  Title                    = {Enzyme recruitment in evolution of new function},
  Author                   = {Jensen, Roy A},
  Journal                  = {Annual Reviews in Microbiology},
  Year                     = {1976},
  Number                   = {1},
  Pages                    = {409--425},
  Volume                   = {30},

  Owner                    = {ranjan},
  Publisher                = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA},
  Timestamp                = {2013.11.30}
}

@Article{Jensen1996,
  Title                    = {Evolutionary recruitment of biochemically specialized subdivisions of Family I within the protein superfamily of aminotransferases.},
  Author                   = {Jensen, Roy A and Gu, Wei},
  Journal                  = {Journal of bacteriology},
  Year                     = {1996},
  Number                   = {8},
  Pages                    = {2161},
  Volume                   = {178},

  Owner                    = {ranjan},
  Publisher                = {American Society for Microbiology (ASM)},
  Timestamp                = {2013.12.04}
}

@Article{Ji2000,
  Title                    = {Buried polar interactions and conformational stability in the simian immunodeficiency virus (SIV) gp41 core.},
  Author                   = {H. Ji and C. Bracken and M. Lu},
  Journal                  = {Biochemistry},
  Year                     = {2000},

  Month                    = {Feb},
  Number                   = {4},
  Pages                    = {676--685},
  Volume                   = {39},

  Abstract                 = {For human (HIV) and simian (SIV) immunodeficiency viruses, the gp41 envelope protein undergoes a receptor-activated conformational change from a labile native structure to an energetically more stable fusogenic conformation, which then mediates viral-cell membrane fusion. The core structure of fusion-active gp41 is a six-helix bundle in which three antiparallel carboxyl-terminal helices are packed against an amino-terminal trimeric coiled coil. Here we show that a recombinant model of the SIV gp41 core, designated N36(L6)C34, forms an alpha-helical trimer that exhibits a cooperative two-state folding-unfolding transition. We investigate the importance of buried polar interactions in determining the overall fold of the gp41 core. We have replaced each of four polar amino acids at the heptad a and d positions of the coiled coil in N36(L6)C34 with a representative hydrophobic amino acid, isoleucine. The Q565I, T582I, and T586I variants form six-helix bundle structures that are 
significantly more stable than that of the wild-type peptide, whereas the Q575I variant misfolds into an insoluble aggregate under physiological conditions. Thus, the buried polar residues within the amino-terminal heptad repeat are important determinants of the structural specificity and stability of the gp41 core. We suggest that these conserved buried polar interactions play a role in governing the conformational state of the gp41 molecule.},
  Institution              = {Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA.},
  Keywords                 = {Amino Acid Sequence; Amino Acid Substitution, genetics; Animals; Circular Dichroism; Glutamine, genetics; Isoleucine, genetics; Macaca; Membrane Glycoproteins, chemistry/genetics; Models, Molecular; Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular; Peptide Fragments, chemistry/genetics; Protein Conformation; Protein Folding; Protein Structure, Secondary; Recombinant Proteins, chemistry; Retroviridae Proteins, chemistry/genetics; Simian immunodeficiency virus, chemistry; Thermodynamics; Threonine, genetics; Viral Envelope Proteins, chemistry/genetics},
  Owner                    = {ranjan},
  Pii                      = {bi991893e},
  Pmid                     = {10651632},
  Timestamp                = {2010.09.22}
}

@Article{Ji2009,
  Title                    = {Evolutionary formation of new protein folds is linked to metallic cofactor recruitment.},
  Author                   = {Hong-Fang Ji and Lei Chen and Ying-Ying Jiang and Hong-Yu Zhang},
  Journal                  = {Bioessays},
  Year                     = {2009},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {975--980},
  Volume                   = {31},

  Abstract                 = {To explore whether the generation of new protein folds could be linked to metallic cofactor recruitment, we identified the oldest examples of folds for manganese, iron, zinc, and copper proteins by analyzing their fold-domain mapping patterns. We discovered that the generation of these folds was tightly coupled to corresponding metals. We found that the emerging order for these folds, i.e., manganese and iron protein folds appeared earlier than zinc and copper counterparts, coincides with the putative bioavailability of the corresponding metals in the ancient anoxic ocean. Therefore, we conclude that metallic cofactors, like organic cofactors, play an evolutionary role in the formation of new protein folds. This link could be explained by the emergence of protein structures with novel folds that could fulfill the new protein functions introduced by the metallic cofactors. These findings not only have important implications for understanding the evolutionary mechanisms of protein 
architectures, but also provide a further interpretation for the evolutionary story of superoxide dismutases.},
  File                     = {Ji2009.pdf:pdfs/Ji2009.pdf:PDF},
  Institution              = {Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, P. R. China.},
  Keywords                 = {Animals; Evolution, Molecular; Metalloproteins, chemistry/genetics/metabolism; Metals, Heavy, metabolism; Protein Binding; Protein Folding; Superoxide Dismutase, metabolism},
  Owner                    = {ranjan},
  Pmid                     = {19644916},
  Timestamp                = {2010.02.06}
}

@Article{Ji2007,
  Title                    = {Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery.},
  Author                   = {Hong-Fang Ji and De-Xin Kong and Liang Shen and Ling-Ling Chen and Bin-Guang Ma and Hong-Yu Zhang},
  Journal                  = {Genome Biol},
  Year                     = {2007},
  Number                   = {8},
  Pages                    = {R176},
  Volume                   = {8},

  Abstract                 = {BACKGROUND: Extant life depends greatly on the binding of small molecules (such as ligands) with macromolecules (such as proteins), and one ligand can bind multiple proteins. However, little is known about the global patterns of ligand-protein mapping. RESULTS: By examining 2,186 well-defined small-molecule ligands and thousands of protein domains derived from a database of druggable binding sites, we show that a few ligands bind tens of protein domains or folds, whereas most ligands bind only one, which indicates that ligand-protein mapping follows a power law. Through assigning the protein-binding orders (early or late) for bio-ligands, we demonstrate that the preferential attachment principle still holds for the power-law relation between ligands and proteins. We also found that polar molecular surface area, H-bond acceptor counts, H-bond donor counts and partition coefficient are potential factors to discriminate ligands from ordinary molecules and to differentiate super 
ligands (shared by three or more folds) from others. CONCLUSION: These findings have significant implications for evolution and drug discovery. First, the chronology of ligand-protein binding can be inferred by the power-law feature of ligand-protein mapping. Some nucleotide-containing ligands, such as ATP, ADP, GDP, NAD, FAD, dihydro-nicotinamide-adenine-dinucleotide phosphate (NDP), nicotinamide-adenine-dinucleotide phosphate (NAP), flavin mononucleotide (FMN) and AMP, are found to be the earliest cofactors bound to proteins, agreeing with the current understanding of evolutionary history. Second, the finding that about 30\% of ligands are shared by two or more domains will help with drug discovery, such as in finding new functions from old drugs, developing promiscuous drugs and depending more on natural products.},
  Institution              = {Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China. jhf@sdut.edu.cn},
  Keywords                 = {Animals; Biogenesis; Drug Design; Evolution, Molecular; Humans; Ligands; Protein Folding; Protein Structure, Tertiary; Proteins, chemistry},
  Owner                    = {ranjan},
  Pii                      = {gb-2007-8-8-r176},
  Pmid                     = {17727706},
  Timestamp                = {2010.02.06}
}

@Article{Jiang2003,
  Title                    = {Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions.},
  Author                   = {Jiang, W. and Li, Z. and Zhang, Z. and Baker, M.L. and Prevelige Jr, P. E. and Chiu, W.},
  Journal                  = {Nat Struct Biol.},
  Year                     = {2003},
  Number                   = {2},
  Pages                    = {131-135},
  Volume                   = {10},

  File                     = {Jiang2003.pdf:pdfs/Jiang2003.pdf:PDF}
}

@Article{Haibao2016,
  Title                    = {Highly stable and self-repairing membrane-mimetic 2D nanomaterials assembled from lipid-like peptoids},
  Author                   = {Haibao Jin and Fang Jiao and Michael D. Daily and Yulin Chen and Feng Yan and Yan-Huai Ding and Xin Zhang and Ellen J. Robertson and Marcel D. Baer and Chun-Long Chen},
  Journal                  = {Nature Communications},
  Year                     = {2016},
  Pages                    = {12252},
  Volume                   = {7},

  Owner                    = {ranjan},
  Timestamp                = {2016.08.19}
}

@Article{Johnson1996,
  Title                    = {Functional implications of protein-protein interactions in icosahedral viruses.},
  Author                   = {J. E. Johnson},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1996},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {27--33},
  Volume                   = {93},

  Abstract                 = {Biological processes often require that a single gene product participate in multiple types of molecular interactions. Viruses with quasiequivalent capsids provide an excellent paradigm for studying such phenomena because identical protein subunits are found in different structural environments. Differences in subunit joints may be controlled by protein segments, duplex or single-stranded RNA, metal ions, or some combination of these. Each of the virus groups examined display a distinctive mechanism for switching interface interactions, illustrating the magnitude of options that are likely to be found in other biological systems. In addition to determining capsid morphology, assembly controls the timing of autocatalytic maturation cleavage of the viral subunits that is required for infectivity in picorna-, noda-, and tetraviruses. The mechanism of assembly-dependent cleavage is conserved in noda- and tetraviruses, although the quaternary structures of the capsids are different 
as are the molecular switches that control subunit interfaces. The function of the cleavage in picorna-, noda-, and tetraviruses is probably to release polypeptides that participate in membrane translocation of RNA.},
  File                     = {Johnson1996.pdf:pdfs/Johnson1996.pdf:PDF},
  Institution              = {Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.},
  Keywords                 = {Amino Acid Sequence; Capsid, chemistry; Macromolecular Substances; Models, Molecular; Molecular Sequence Data; Protein Binding; RNA Viruses, chemistry/ultrastructure; RNA, Viral, chemistry; Viral Proteins, chemistry; Virus Replication},
  Owner                    = {ranjan},
  Pmid                     = {8552620},
  Timestamp                = {2009.07.07}
}

@Article{Johnson1997,
  Title                    = {Quasi-equivalent viruses: a paradigm for protein assemblies},
  Author                   = {Johnson, J. E. and Speir, J. A.},
  Journal                  = JMB,
  Year                     = {1997},
  Number                   = {5},
  Pages                    = {665--675},
  Volume                   = {269},

  File                     = {Johnson1997.pdf:pdfs/Johnson1997.pdf:PDF}
}

@Article{Jong1998,
  Title                    = {Genealogy of the alpha-crystallin--small heat-shock protein superfamily.},
  Author                   = {W. W. de Jong and G. J. Caspers and J. A. Leunissen},
  Journal                  = {Int J Biol Macromol},
  Year                     = {1998},
  Number                   = {3-4},
  Pages                    = {151--162},
  Volume                   = {22},

  Abstract                 = {Sequences of 40 very diverse representatives of the alpha-crystallin-small heat-shock protein (alpha-Hsp) superfamily are compared. Their characteristic C-terminal 'alpha-crystallin domain' of 80-100 residues contains short consensus sequences that are highly conserved from prokaryotes to eukaryotes. There are, in addition, some positions that clearly distinguish animal from non-animal alpha-Hsps. The alpha-crystallin domain is predicted to consist of two hydrophobic beta-sheet motifs, separated by a hydrophilic region which is variable in length. Combination of a conserved alpha-crystallin domain with a variable N-terminal domain and C-terminal extension probably modulates the properties of the various alpha-Hsps as stress-protective and structural oligomeric proteins. Phylogeny reconstruction indicates that multiple alpha-Hsps were already present in the last common ancestor of pro- and eukaryotes. It is suggested that during eukaryote evolution, animal and non-animal alpha-
Hsps originated from different ancestral gene copies. Repeated gene duplications gave rise to the multiple alpha-Hsps present in most organisms.},
  Institution              = {Department of Biochemistry, University of Nijmegen, The Netherlands. w.dejong@bioch.kun.NL},
  Keywords                 = {Amino Acid Sequence; Animals; Conserved Sequence; Crystallins, chemistry/genetics/physiology; Evolution, Molecular; Gene Expression; Heat-Shock Proteins, chemistry/genetics/physiology; Humans; Mammals; Molecular Sequence Data; Multigene Family; Phylogeny; Protein Structure, Secondary; Sequence Homology, Amino Acid; Vertebrates},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9650070},
  Timestamp                = {2011.09.15}
}

@Article{Joosten2011,
  Title                    = {A series of PDB related databases for everyday needs.},
  Author                   = {Joosten, Robbie P. and {te Beek}, Tim A H. and Krieger, Elmar and Hekkelman, Maarten L. and Hooft, Rob W W. and Schneider, Reinhard and Sander, Chris and Vriend, Gert},
  Journal                  = {Nucleic Acids Res},
  Year                     = {2011},

  Month                    = {Jan},
  Number                   = {Database issue},
  Pages                    = {D411--D419},
  Volume                   = {39},

  Abstract                 = {The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB. Each database holds one entry, if possible, for each PDB entry. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems. PDB_REDO holds re-refined, and often improved, copies of all structures solved by X-ray. WHY_NOT summarizes why certain files could not be produced. All these systems are updated weekly. The data sets can be used for the analysis of properties of protein structures in areas ranging from structural genomics, to cancer biology and protein design.},
  Doi                      = {10.1093/nar/gkq1105},
  Institution              = {Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.},
  Keywords                 = {Databases, Protein; Protein Conformation; Protein Structure, Secondary; Proteins, chemistry; Sequence Alignment; Sequence Analysis, Protein; Systems Integration; User-Computer Interface},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {gkq1105},
  Pmid                     = {21071423},
  Timestamp                = {2014.05.11}
}

@Article{Jordan2005,
  Title                    = {A universal trend of amino acid gain and loss in protein evolution.},
  Author                   = {I. King Jordan and Fyodor A Kondrashov and Ivan A Adzhubei and Yuri I Wolf and Eugene V Koonin and Alexey S Kondrashov and Shamil Sunyaev},
  Journal                  = {Nature},
  Year                     = {2005},

  Month                    = {Feb},
  Number                   = {7026},
  Pages                    = {633--638},
  Volume                   = {433},

  Abstract                 = {Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G + C)-rich (or (A + T)-rich) genomes contain more (or fewer) amino acids encoded by (G + C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, 
except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.},
  Institution              = {National Center for Biotechnology Information, NIH, Bethesda, Maryland 20894, USA.},
  Keywords                 = {AT Rich Sequence, genetics; Amino Acid Substitution, genetics; Amino Acids, genetics; Animals; Archaea, genetics; Bacteria, genetics; Base Composition; Eukaryotic Cells, metabolism; Evolution, Molecular; GC Rich Sequence, genetics; Genome; Humans; Phylogeny; Polymorphism, Single Nucleotide, genetics; Prokaryotic Cells, metabolism; Proteins, chemistry/genetics},
  Owner                    = {ranjan},
  Pii                      = {nature03306},
  Pmid                     = {15660107},
  Timestamp                = {2010.06.26}
}

@Article{tip3p,
  Title                    = {{Comparison of simple potential functions for simulating liquid water}},
  Author                   = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
  Journal                  = {J. Chem. Phys.},
  Year                     = {1983},
  Pages                    = {926},
  Volume                   = {79}
}

@Article{Jukes1993,
  Title                    = {Evolutionary changes in the genetic code.},
  Author                   = {T. H. Jukes and S. Osawa},
  Journal                  = {Comp Biochem Physiol B},
  Year                     = {1993},

  Month                    = {Nov},
  Number                   = {3},
  Pages                    = {489--494},
  Volume                   = {106},

  Abstract                 = {1. The genetic code was thought to be identical ("universal") in all biological systems until 1981, when it was discovered that the coding system in mammalian mitochondria differed from the universal code in the use of codons AUA, UGA, AGA and AGG. 2. Many other differences have since been discovered, some in mitochondria of various phyla, others in bacteria, ciliated protozoa, algae and yeasts. 3. The original thesis that the code was universal and "frozen" depended on the precept that any mutational change in the code would be lethal, because it would produce widespread alterations in the amino acid sequences of proteins. Such changes would destroy protein function, and hence would be intolerable. 4. The objection was "by-passed" by nature. It is possible for a codon to disappear from mRNA molecules, often as a result of directional mutation pressure in DNA: thus all UGA stop codons can be replaced by UAA. 5. The missing UGA codon can then reappear when some UGG tryptophan 
codons mutate to UGA. The new UGA codons will be translated as tryptophan, as is the case in non-plant mitochondria and Mycoplasma. Therefore, no changes have taken place in the amino acid sequences of proteins. 6. Variations of this procedure have occurred, affecting various codons, and discoveries are still being made. The findings illustrate the evolutionary interplay between tRNA, release factors and codon-anticodon pairing.},
  Institution              = {Space Sciences Laboratory, University of California, Berkeley 94720.},
  Keywords                 = {Animals; Anticodon; Biological Evolution; Codon; Genetic Code; Mitochondria, physiology; Mycoplasma, genetics; Plants, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {8281749},
  Timestamp                = {2011.09.16}
}

@Article{Kabsch1983,
  Title                    = {Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.},
  Author                   = {Kabsch, W. and Sander, C.},
  Journal                  = {Biopolymers},
  Year                     = {1983},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {2577--2637},
  Volume                   = {22},

  Doi                      = {10.1002/bip.360221211},
  Keywords                 = {Amino Acid Sequence; Hydrogen Bonding; Protein Conformation; Proteins},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {6667333},
  Timestamp                = {2014.05.11}
}

@Article{Kanehisa2003,
  Title                    = {Bioinformatics in the post-sequence era},
  Author                   = {Kanehisa, Minoru and Bork, Peer},
  Journal                  = {nature genetics},
  Year                     = {2003},
  Pages                    = {305--310},
  Volume                   = {33},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2016.07.17}
}

@Article{Karplus2002,
  Title                    = {Molecular dynamics simulations of biomolecules.},
  Author                   = {Karplus, Martin and McCammon, J Andrew},
  Journal                  = {Nat Struct Biol},
  Year                     = {2002},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {646--652},
  Volume                   = {9},

  Abstract                 = {Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. The early view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational changes play an essential role in their function. This review presents a brief description of the origin and early uses of biomolecular simulations. It then outlines some recent studies that illustrate the utility of such simulations and closes with a discussion of their ever-increasing potential for contributing to biology.},
  Doi                      = {10.1038/nsb0902-646},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA. marci@tammy.harvard.edu},
  Keywords                 = {Models, Molecular; Protein Conformation},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nsb0902-646},
  Pmid                     = {12198485},
  Timestamp                = {2014.02.07}
}

@Article{Karplus1981,
  Title                    = {The internal dynamics of globular protein},
  Author                   = {Karplus, Martin and McCammon, J Andrew and Peticolas, Warner L},
  Journal                  = {Critical Reviews in Biochemistry and Molecular Biology},
  Year                     = {1981},
  Number                   = {4},
  Pages                    = {293--349},
  Volume                   = {9},

  Owner                    = {ranjan},
  Publisher                = {Informa UK Ltd UK},
  Timestamp                = {2014.08.20}
}

@Article{Kastritis2013,
  Title                    = {On the binding affinity of macromolecular interactions: daring to ask why proteins interact},
  Author                   = {Kastritis, Panagiotis L and Bonvin, Alexandre MJJ},
  Journal                  = {Journal of The Royal Society Interface},
  Year                     = {2013},
  Number                   = {79},
  Volume                   = {10},

  Owner                    = {ranjan},
  Publisher                = {The Royal Society},
  Timestamp                = {2013.11.18}
}

@Article{Kato2007,
  Title                    = {Xenobiotic transporter-adaptor network.},
  Author                   = {Yukio Kato},
  Journal                  = {Drug Metab Pharmacokinet},
  Year                     = {2007},

  Month                    = {Dec},
  Number                   = {6},
  Pages                    = {401--408},
  Volume                   = {22},

  Abstract                 = {Many types of xenobiotic transporters have been identified. They generally exhibit multispecific recognition of various types of substrates, and mediate membrane permeation of therapeutic agents, thereby playing important roles in drug absorption and disposition. It has recently been proposed that protein-protein interactions involving the xenobiotic transporters may affect their function, localization and expression on plasma membranes. So-called adaptor proteins that directly interact with the transporters include PDZ domain-containing proteins (PSD95, Dlg and ZO1). These PDZ adaptors have multiple PDZ domains in their structure, and each PDZ domain can interact with the cytosolic region of the transporters, and so it has been hypothesized that transporters are localized within networks consisting of several transporters and adaptors. Interaction with a PDZ adaptor is essential for the cell-surface localization of at least some xenobiotic transporters, and therefore, such 
interaction could be required for efficiency and fidelity in the vectorial transport of xenobiotics and therapeutic agents in epithelial cells. This review article summarizes recent evidence on the interactions of xenobiotic transporters with adaptor proteins, and presents a working hypothesis concerning their pharmacological significance.},
  Institution              = {Division of Pharmaceutical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan. ykato@p.kanazawa-u.ac.jp},
  Keywords                 = {Adaptor Proteins, Signal Transducing, chemistry/metabolism; Animals; Binding Sites; Biological Transport; Cell Membrane, metabolism; Humans; Membrane Transport Proteins, chemistry/metabolism; PDZ Domains; Pharmacokinetics; Protein Binding; Protein Conformation; Xenobiotics, metabolism},
  Owner                    = {ranjan},
  Pii                      = {JST.JSTAGE/dmpk/22.401},
  Pmid                     = {18159127},
  Timestamp                = {2009.06.21}
}

@Article{Kauffman1986,
  Title                    = {Autocatalytic sets of proteins.},
  Author                   = {Kauffman, S. A.},
  Journal                  = {J Theor Biol},
  Year                     = {1986},

  Month                    = {Mar},
  Number                   = {1},
  Pages                    = {1--24},
  Volume                   = {119},

  Abstract                 = {This article investigates the possibility that the emergence of reflexively autocatalytic sets of peptides and polypeptides may be an essentially inevitable collective property of any sufficiently complex set of polypeptides. The central idea is based on the connectivity properties of random directed graphs. In the set of amino acid monomer and polymer species up to some maximum length, M, the number of possible polypeptides is large, but, for specifiable "legitimate" end condensation, cleavage and transpeptidation exchange reactions, the number of potential reactions by which the possible polypeptides can interconvert is very much larger. A directed graph in which arrows from smaller fragments to larger condensation products depict potential synthesis reactions, while arrows from the larger peptide to the smaller fragments depict the reverse cleavage reactions, comprises the reaction graph for such a system. Polypeptide protoenzymes are able to catalyze such reactions. The 
distribution of catalytic capacities in peptide space is a fundamental problem in its own right, and in its bearing on the existence of autocatalytic sets of proteins. Using an initial idealized hypothesis that an arbitrary polypeptide has a fixed a priori probability of catalyzing any arbitrary legitimate reaction to assign to each polypeptide those reactions, if any, which it catalyzes, the probability that the set of polypeptides up to length M contains a reflexively autocatalytic subset can be calculated and is a percolation problem on such reaction graphs. Because, as M increases, the ratio of reactions among the possible polypeptides to polypeptides rises rapidly, the existence of such autocatalytic subsets is assured for any fixed probability of catalysis. The main conclusions of this analysis appear independent of the idealizations of the initial model, introduce a novel kind of parallel selection for peptides catalyzing connected sequences of reactions, depend upon a new kind of minimal critical 
complexity whose properties are definable, and suggest that the emergence of self replicating systems may be a self organizing collective property of critically complex protein systems in prebiotic evolution. Similar principles may apply to the emergence of a primitive connected metabolism. Recombinant DNA procedures, cloning random DNA coding sequences into expression vectors, afford a direct avenue to test the distribution of catalytic capacities in peptide space, may provide a new means to select or screen for peptides with useful properties, and may ultimately lead toward the actual construction of autocatalytic peptide sets.},
  Keywords                 = {Amino Acids, metabolism; Catalysis; Kinetics; Models, Biological; Peptide Biosynthesis; Polymers, biosynthesis; Probability; Protein Biosynthesis; Protein Conformation},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {3713221},
  Timestamp                = {2012.04.05}
}

@Article{Ke2012,
  Title                    = {Three-dimensional structures self-assembled from DNA bricks},
  Author                   = {Ke, Yonggang and Ong, Luvena L and Shih, William M and Yin, Peng},
  Journal                  = {Science},
  Year                     = {2012},
  Number                   = {6111},
  Pages                    = {1177--1183},
  Volume                   = {338},

  Owner                    = {ranjan},
  Publisher                = {American Association for the Advancement of Science},
  Timestamp                = {2015.03.22}
}

@Article{Keef2006,
  Title                    = {Master equation approach to the assembly of viral capsids},
  Author                   = {Keef, T. and Micheletti, C. and Twarock, R.},
  Journal                  = {J. Theor. Biol.},
  Year                     = {2006},
  Number                   = {3},
  Pages                    = {713--721},
  Volume                   = {242},

  File                     = {Keef2006.pdf:pdfs/Keef2006.pdf:PDF}
}

@Article{Keef2005,
  Title                    = {Assembly models for Papovaviridae based on tiling theory},
  Author                   = {Keef, T. and Taormina, A. and Twarock, R.},
  Journal                  = {Phys. Biol.},
  Year                     = {2005},
  Number                   = {3},
  Pages                    = {175--188},
  Volume                   = {2},

  File                     = {Keef2005.pdf:pdfs/Keef2005.pdf:PDF}
}

@Article{Keefe2001,
  Title                    = {Functional proteins from a random-sequence library},
  Author                   = {Keefe, Anthony D and Szostak, Jack W},
  Journal                  = {Nature},
  Year                     = {2001},
  Number                   = {6829},
  Pages                    = {715--718},
  Volume                   = {410},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2013.08.18}
}

@Article{Kendrew1958,
  Title                    = {A three-dimensional model of the myoglobin molecule obtained by x-ray analysis.},
  Author                   = {Kendrew, J. C. and Bodo, G. and Dintzis, H. M. and Parrish, R. G. and Wyckoff, H. and Phillips, D. C.},
  Journal                  = {Nature},
  Year                     = {1958},

  Month                    = {Mar},
  Number                   = {4610},
  Pages                    = {662--666},
  Volume                   = {181},

  Keywords                 = {Hemoglobins},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {13517261},
  Timestamp                = {2013.11.12}
}

@Article{Kennicutt1990,
  Title                    = {Unusual normal alkane distributions in offshore New Zealand sediments},
  Author                   = {Kennicutt, Mahlon C. and Brooks, James M.},
  Journal                  = {Organic Geochemistry},
  Year                     = {1990},

  Month                    = {Jan},
  Number                   = {2},
  Pages                    = {193-197},
  Volume                   = {15},

  Doi                      = {10.1016/0146-6380(90)90083-C},
  Owner                    = {ranjan},
  Publisher                = {Elsevier },
  Timestamp                = {2014.01.17}
}

@Misc{Kerner2005,
  Title                    = {Combinatorial rules of icosahedral capsid growth},

  Author                   = {Kerner,R.},
  Year                     = {2005},

  File                     = {Kerner2005.pdf:pdfs/Kerner2005.pdf:PDF}
}

@Article{Kersey2010,
  Title                    = {Ensembl Genomes: extending Ensembl across the taxonomic space.},
  Author                   = {P. J. Kersey and D. Lawson and E. Birney and P. S. Derwent and M. Haimel and J. Herrero and S. Keenan and A. Kerhornou and G. Koscielny and A. K\"{a}h\"{a}ri and R. J. Kinsella and E. Kulesha and U. Maheswari and K. Megy and M. Nuhn and G. Proctor and D. Staines and F. Valentin and A. J. Vilella and A. Yates},
  Journal                  = {Nucleic Acids Res},
  Year                     = {2010},

  Month                    = {Jan},
  Number                   = {Database issue},
  Pages                    = {D563--D569},
  Volume                   = {38},

  Abstract                 = {Ensembl Genomes (http://www.ensemblgenomes.org) is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community, which we consider as essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimised data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. 
data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.},
  Institution              = {EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK. pkersey@ebi.ac.uk},
  Keywords                 = {Animals; Computational Biology, methods/trends; Databases, Genetic; Databases, Nucleic Acid; Gene Expression; Genome, Bacterial; Genome, Fungal; Genome, Plant; Information Storage and Retrieval, methods; Internet; Invertebrates, genetics; Polymorphism, Genetic; Protein Structure, Tertiary; Software},
  Owner                    = {ranjan},
  Pii                      = {gkp871},
  Pmid                     = {19884133},
  Timestamp                = {2010.05.08}
}

@Article{Keskin2007,
  Title                    = {Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies.},
  Author                   = {Keskin, Ozlem},
  Journal                  = {BMC Struct Biol},
  Year                     = {2007},
  Pages                    = {31},
  Volume                   = {7},

  Abstract                 = {How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium.Here, two antibodies, a germline antibody of 36-65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM) is used in the calculations. Pre-existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins 
are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones.Results suggest that the pre-equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.},
  Doi                      = {10.1186/1472-6807-7-31},
  Institution              = {Koc University, Center for Computational Biology and Bioinformatics and College of Engineering, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey. okeskin@ku.edu.tr},
  Keywords                 = {Antibodies, chemistry/metabolism; Antigens, chemistry/metabolism; Binding Sites; Ligands; Protein Binding; Protein Conformation; Protein Structure, Secondary; Temperature},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {1472-6807-7-31},
  Pmid                     = {17509130},
  Timestamp                = {2013.12.14}
}

@Article{Kesten1964,
  Title                    = {On the Number of Self-Avoiding Walks. II},
  Author                   = {Kesten, Harry},
  Journal                  = {Journal of Mathematical Physics},
  Year                     = {1964},
  Pages                    = {1128},
  Volume                   = {5},

  Owner                    = {ranjan},
  Timestamp                = {2013.07.06}
}

@Article{Kesten1963,
  Title                    = {On the Number of Self-Avoiding Walks},
  Author                   = {Kesten, Harry},
  Journal                  = {Journal of Mathematical Physics},
  Year                     = {1963},
  Pages                    = {960},
  Volume                   = {4},

  Owner                    = {ranjan},
  Timestamp                = {2013.07.06}
}

@Article{Khan2010,
  Title                    = {Performance of protein stability predictors.},
  Author                   = {Sofia Khan and Mauno Vihinen},
  Journal                  = {Hum Mutat},
  Year                     = {2010},

  Month                    = {Jun},
  Number                   = {6},
  Pages                    = {675--684},
  Volume                   = {31},

  Abstract                 = {Stability is a fundamental property affecting function, activity, and regulation of biomolecules. Stability changes are often found for mutated proteins involved in diseases. Stability predictors computationally predict protein-stability changes caused by mutations. We performed a systematic analysis of 11 online stability predictors' performances. These predictors are CUPSAT, Dmutant, FoldX, I-Mutant2.0, two versions of I-Mutant3.0 (sequence and structure versions), MultiMutate, MUpro, SCide, Scpred, and SRide. As input, 1,784 single mutations found in 80 proteins were used, and these mutations did not include those used for training. The programs' performances were also assessed according to where the mutations were found in the proteins, that is, in secondary structures and on the surface or in the core of a protein, and according to protein structure type. The extents to which the mutations altered the occupied volumes at the residue sites and the charge interactions were 
also characterized. The predictions of all programs were in line with the experimental data. I-Mutant3.0 (utilizing structural information), Dmutant, and FoldX were the most reliable predictors. The stability-center predictors performed with similar accuracy. However, at best, the predictions were only moderately accurate ( approximately 60\%) and significantly better tools would be needed for routine analysis of mutation effects.},
  Institution              = {Institute of Medical Technology, FI-33014 University of Tampere, Finland.},
  Keywords                 = {Algorithms; Computational Biology, methods; Databases, Protein; Mutation; Protein Stability; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins, chemistry/genetics; Reproducibility of Results; Software},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {20232415},
  Timestamp                = {2011.09.30}
}

@Article{Khersonsky2006,
  Title                    = {Enzyme promiscuity: evolutionary and mechanistic aspects},
  Author                   = {Khersonsky, Olga and Roodveldt, Cintia and Tawfik, Dan S},
  Journal                  = {Current opinion in chemical biology},
  Year                     = {2006},
  Number                   = {5},
  Pages                    = {498--508},
  Volume                   = {10},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.19}
}

@Article{Khersonsky2010,
  Title                    = {Enzyme promiscuity: a mechanistic and evolutionary perspective.},
  Author                   = {Olga Khersonsky and Dan S Tawfik},
  Journal                  = {Annu Rev Biochem},
  Year                     = {2010},
  Pages                    = {471--505},
  Volume                   = {79},

  Abstract                 = {Many, if not most, enzymes can promiscuously catalyze reactions, or act on substrates, other than those for which they evolved. Here, we discuss the structural, mechanistic, and evolutionary implications of this manifestation of infidelity of molecular recognition. We define promiscuity and related phenomena and also address their generality and physiological implications. We discuss the mechanistic enzymology of promiscuity--how enzymes, which generally exert exquisite specificity, catalyze other, and sometimes barely related, reactions. Finally, we address the hypothesis that promiscuous enzymatic activities serve as evolutionary starting points and highlight the unique evolutionary features of promiscuous enzyme functions.},
  File                     = {Khersonsky2010.pdf:pdfs/Khersonsky2010.pdf:PDF},
  Institution              = {Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.},
  Keywords                 = {Catalysis; Catalytic Domain; Enzymes, chemistry/genetics/metabolism; Evolution, Molecular; Humans; Substrate Specificity},
  Owner                    = {ranjan},
  Pmid                     = {20235827},
  Timestamp                = {2011.03.03}
}

@Article{Khoury2014,
  Title                    = {Protein folding and de novo protein design for biotechnological applications},
  Author                   = {Khoury, George A and Smadbeck, James and Kieslich, Chris A and Floudas, Christodoulos A},
  Journal                  = {Trends in biotechnology},
  Year                     = {2014},
  Number                   = {2},
  Pages                    = {99--109},
  Volume                   = {32},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2015.03.22}
}

@Article{Kim2009,
  Title                    = {Probing interfacial equilibration in microsphere crystals formed by DNA-directed assembly},
  Author                   = {Kim, Anthony J and Scarlett, Raynaldo and Biancaniello, Paul L and Sinno, Talid and Crocker, John C},
  Journal                  = {Nature materials},
  Year                     = {2009},
  Number                   = {1},
  Pages                    = {52--55},
  Volume                   = {8},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2015.04.20}
}

@Article{Kim2005,
  Title                    = {Evolutionary perspectives on innate immunity from the study of Caenorhabditis elegans.},
  Author                   = {Dennis H Kim and Frederick M Ausubel},
  Journal                  = {Curr Opin Immunol},
  Year                     = {2005},

  Month                    = {Feb},
  Number                   = {1},
  Pages                    = {4--10},
  Volume                   = {17},

  Abstract                 = {Genetic and functional genomic approaches have begun to define the molecular determinants of pathogen resistance in Caenorhabditis elegans. Conserved signal transduction components are required for pathogen resistance, including a Toll/IL-1 receptor domain adaptor protein that functions upstream of a conserved p38 MAP kinase pathway. We suggest that this pathway is an ancestral innate immune signaling pathway present in the common ancestor of nematodes, arthropods and vertebrates, which is likely to predate the involvement of canonical Toll signaling pathways in innate immunity. We anticipate that the study of pathogen resistance in C. elegans will continue to provide evolutionary and mechanistic insights into the signal transduction and physiology of innate immunity.},
  Institution              = {Department of Genetics, Harvard Medical School, and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.},
  Keywords                 = {Animals; Caenorhabditis elegans Proteins, genetics/immunology; Caenorhabditis elegans, genetics/immunology; Evolution; Genes, Helminth, genetics/immunology; Immunity, Innate; MAP Kinase Signaling System, genetics/immunology},
  Owner                    = {ranjan},
  Pii                      = {S0952-7915(04)00189-X},
  Pmid                     = {15653303},
  Timestamp                = {2010.04.20}
}

@Article{Kim2008,
  Title                    = {The role of disorder in interaction networks: a structural analysis},
  Author                   = {Kim, Philip M and Sboner, Andrea and Xia, Yu and Gerstein, Mark},
  Journal                  = {Molecular Systems Biology},
  Year                     = {2008},
  Number                   = {1},
  Volume                   = {4},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2013.12.06}
}

@Article{Kimura1989,
  Title                    = {The neutral theory of molecular evolution and the world view of the neutralists},
  Author                   = {Kimura, Motoo},
  Journal                  = {Genome},
  Year                     = {1989},
  Number                   = {1},
  Pages                    = {24--31},
  Volume                   = {31},

  Owner                    = {ranjan},
  Publisher                = {NRC Research Press},
  Timestamp                = {2013.12.01}
}

@Article{Kimura1981,
  Title                    = {Possibility of extensive neutral evolution under stabilizing selection with special reference to nonrandom usage of synonymous codons.},
  Author                   = {M. Kimura},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1981},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {5773--5777},
  Volume                   = {78},

  Abstract                 = {The rate of evolution in terms of the number of mutant substitutions in a finite population is investigated assuming a quantitative character subject to stabilizing selection, which is known to be the most prevalent type of natural selection. It is shown that, if a large number of segregating loci (or sites) are involved, the average selection coefficient per mutant under stabilizing selection may be exceedingly small. These mutants are very slightly deleterious but nearly neutral, so that mutant substitutions are mainly controlled by random drift, although the rate of evolution may be lower as compared with the situation in which all the mutations are strictly neutral. This is treated quantitatively by using the diffusion equation method in population genetics. A model of random drift under stabilizing selection is then applied to the problem of "nonrandom" or unequal usage of synonymous codons, and it is shown that such nonrandomness can readily be understood within the 
framework of the neutral mutation--random drift hypothesis (the neutral theory, for short) of molecular evolution.},
  Keywords                 = {Alleles; Biological Evolution; Codon; Gene Frequency; Mutation; Phenotype; Probability; RNA, Messenger; Selection, Genetic},
  Owner                    = {ranjan},
  Pmid                     = {6946514},
  Timestamp                = {2011.04.26}
}

@Article{Kimura1979,
  Title                    = {Model of effectively neutral mutations in which selective constraint is incorporated.},
  Author                   = {M. Kimura},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1979},

  Month                    = {Jul},
  Number                   = {7},
  Pages                    = {3440--3444},
  Volume                   = {76},

  Abstract                 = {Based on the idea that selective neutrality is the limit when the selective disadvantage becomes indefinitely small, a model of neutral (and nearly neutral) mutations is proposed that assumes that the selection coefficient (s') against the mutant at various sites within a cistron (gene) follows a Gamma distribution; f(s') = alpha(beta)e(-alphas')s'(beta-1)/Gamma(beta), in which alpha = beta/ s' and s' is the mean selection coefficient against the mutants ( s' > 0; 1 [unk] beta > 0). The mutation rate for alleles whose selection coefficients s' lie in the range between 0 and 1/(2N(e)), in which N(e) is the effective population size, is termed the effectively neutral mutation rate (denoted by v(e)). Using the model of "infinite sites" in population genetics, formulas are derived giving the average heterozygosity ( h(e)) and evolutionary rate per generation (k(g)) in terms of mutant substitutions. It is shown that, with parameter values such as beta = 0.5 and s' = 0.001, the 
average heterozygosity increases much more slowly as N(e) increases, compared with the case in which a constant fraction of mutations are neutral. Furthermore, the rate of evolution per year (k(1)) becomes constant among various organisms, if the generation span (g) in years is inversely proportional to radicalN(e) among them and if the mutation rate per generation is constant. Also, it is shown that we have roughly k(g) = v(e). The situation becomes quite different if slightly advantageous mutations occur at a constant rate independent of environmental conditions. In this case, the evolutionary rate can become enormously higher in a species with a very large population size than in a species with a small population size, contrary to the observed pattern of evolution at the molecular level.},
  Institution              = {National Institute of Genetics, Mishima 411, Japan.},
  Owner                    = {ranjan},
  Pmid                     = {16592684},
  Timestamp                = {2011.04.26}
}

@Article{Kimura1968,
  Title                    = {Evolutionary rate at the molecular level.},
  Author                   = {M. Kimura},
  Journal                  = {Nature},
  Year                     = {1968},

  Month                    = {Feb},
  Number                   = {5129},
  Pages                    = {624--626},
  Volume                   = {217},

  Keywords                 = {Amino Acid Sequence; Animals; Biological Evolution; Cytochromes; DNA; Gene Frequency; Genetics, Population; Haploidy; Humans; Mathematics; Mutation; Nucleotides},
  Owner                    = {ranjan},
  Pmid                     = {5637732},
  Timestamp                = {2011.04.26}
}

@Article{Kimura1974,
  Title                    = {On some principles governing molecular evolution.},
  Author                   = {M. Kimura and T. Ota},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1974},

  Month                    = {Jul},
  Number                   = {7},
  Pages                    = {2848--2852},
  Volume                   = {71},

  Abstract                 = {THE FOLLOWING FIVE PRINCIPLES WERE DEDUCED FROM THE ACCUMULATED EVIDENCE ON MOLECULAR EVOLUTION AND THEORETICAL CONSIDERATIONS OF THE POPULATION DYNAMICS OF MUTANT SUBSTITUTIONS: (i) for each protein, the rate of evolution in terms of amino acid substitutions is approximately constant/site per year for various lines, as long as the function and tertiary structure of the molecule remain essentially unaltered. (ii) Functionally less important molecules or parts of a molecule evolve (in terms of mutant substitutions) faster than more important ones. (iii) Those mutant substitutions that disrupt less the existing structure and function of a molecule (conservative substitutions) occur more frequently in evolution than more disruptive ones. (iv) Gene duplication must always precede the emergence of a gene having a new function. (v) Selective elimination of definitely deleterious mutants and random fixation of selectively neutral or very slightly deleterious mutants occur far more 
frequently in evolution than positive Darwinian selection of definitely advantageous mutants.},
  Keywords                 = {Biological Evolution; Genetic Code; Genetics, Population; Molecular Biology; Mutation; Selection, Genetic},
  Owner                    = {ranjan},
  Pmid                     = {4527913},
  Timestamp                = {2011.04.26}
}

@Article{King1977,
  Title                    = {Symbiosis and the origin of life.},
  Author                   = {King, G. A.},
  Journal                  = {Orig Life},
  Year                     = {1977},

  Month                    = {Apr},
  Number                   = {1},
  Pages                    = {39--53},
  Volume                   = {8},

  Abstract                 = {The paper uses chemical kinetic arguments and illustrations by computer modelling to discuss the origin and evolution of life. Complex self-reproducing chemical systems cannot arise spontaneously, whereas simple auto-catalytic systems can, especially in an irradiated aqueous medium. Self-reproducing chemical particles of any complexity, in an appropriate environment, have a self-regulating property which permits long-term survival. However, loss of materials from the environment can lead to continuing decay which is circumvented by physical union between different kinds of self-reproducing particles. The increasing complexity produced by such unions (symbioses) is irreversible so that the chemical system evolves. It is suggested that evolution by successive symbioses brought about the change from simple, spontaneously arising, auto-catalytic particles to complex prokaryotic cells.},
  Keywords                 = {Biogenesis; Biological Evolution; Computers; Kinetics; Mathematics; Models, Theoretical; Symbiosis},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {896191},
  Timestamp                = {2012.04.05}
}

@Article{King1969,
  Title                    = {Non-Darwinian evolution.},
  Author                   = {J. L. King and T. H. Jukes},
  Journal                  = {Science},
  Year                     = {1969},

  Month                    = {May},
  Number                   = {881},
  Pages                    = {788--798},
  Volume                   = {164},

  Keywords                 = {Alleles; Amino Acid Sequence; Animals; Biological Evolution; Cytochromes; DNA; Genetic Code; Hemoglobins; Humans; Molecular Biology; Mutation; Proteins; Selection, Genetic},
  Owner                    = {ranjan},
  Pmid                     = {5767777},
  Timestamp                = {2011.04.28}
}

@Article{Kini1998,
  Title                    = {Proline brackets and identification of potential functional sites in proteins: toxins to therapeutics.},
  Author                   = {R. M. Kini},
  Journal                  = {Toxicon},
  Year                     = {1998},

  Month                    = {Nov},
  Number                   = {11},
  Pages                    = {1659--1670},
  Volume                   = {36},

  Abstract                 = {Protein toxins induce their specific pharmacological effects through protein protein interaction. Identification of these protein-protein interaction sites could lead to prototypes of highly specific therapeutic agents. However, deciphering the structure function relationships of protein toxins and locating the functional sites is a difficult, tedious and cumbersome task. We recently developed a novel predictive method to identify potential protein protein interaction sites directly from the amino acid sequence of a protein (R. M. Kini and H. J. Evans (1996) FEBS Lett. 385, 81-86) based on the presence of proline residues, a common residue found predominantly in the flanking segments of protein-protein interaction sites (R. M. Kini and H. J. Evans (1996) Biochem. Biophys. Res. Commun. 212, 1115-1124). It is a simple and straight-forward method. This review describes the new method and its application to solve structure function relationships of protein toxins. The method is 
useful in identifying functional sites in toxins, despite the subtle and complex nature of their structure function relationships and saves significant amounts of time and money.},
  File                     = {Kini1998.pdf:pdfs/Kini1998.pdf:PDF},
  Institution              = {Bioscience Centre, Faculty of Science, National University of Singapore, Singapore.},
  Keywords                 = {Amino Acid Sequence; Amino Acids, chemistry; Animals; Binding Sites; Calcium Channel Blockers, chemistry/pharmacology; Elapid Venoms, chemistry/pharmacology; Molecular Sequence Data; Proline, chemistry/pharmacology; Protein Binding; Protein Conformation; Rats; Sequence Homology, Amino Acid; Structure-Activity Relationship; Toxins, Biological, chemistry/pharmacology},
  Owner                    = {ranjan},
  Pii                      = {S0041-0101(98)00159-7},
  Pmid                     = {9792183},
  Timestamp                = {2009.08.08}
}

@Other{Kirkpatrick1983,
  author    = {Kirkpatrick, S. and Gelatt, C. D. and Vecchi, M. P.},
  title     = {Optimization by simulated annealing},
  year      = {1983},
  owner     = {ranjan},
  timestamp = {2016.09.04},
}

@Article{Klug1987,
  Title                    = {Zinc fingers: a novel protein motif for nucleic acid recognition},
  Author                   = {Klug, Aaron and Rhodes, Daniela},
  Journal                  = {Trends in Biochemical Sciences},
  Year                     = {1987},
  Pages                    = {464--469},
  Volume                   = {12},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.17}
}

@Article{Knight2015,
  Title                    = {Sequence Programmable Peptoid Polymers for Diverse Materials Applications},
  Author                   = {Knight, Abigail S and Zhou, Effie Y and Francis, Matthew B and Zuckermann, Ronald N},
  Journal                  = {Advanced Materials},
  Year                     = {2015},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2015.07.13}
}

@Article{Knowles2010,
  Title                    = {Nanostructured films from hierarchical self-assembly of amyloidogenic proteins},
  Author                   = {Knowles, Tuomas PJ and Oppenheim, Tomas W and Buell, Alexander K and Chirgadze, Dimitri Y and Welland, Mark E},
  Journal                  = {Nature nanotechnology},
  Year                     = {2010},
  Number                   = {3},
  Pages                    = {204--207},
  Volume                   = {5},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2015.05.28}
}

@Article{Koehl1999,
  Title                    = {De novo protein design. I. In search of stability and specificity.},
  Author                   = {P. Koehl and M. Levitt},
  Journal                  = {J Mol Biol},
  Year                     = {1999},

  Month                    = {Nov},
  Number                   = {5},
  Pages                    = {1161--1181},
  Volume                   = {293},

  Abstract                 = {We have developed a fully automated protein design strategy that works on the entire sequence of the protein and uses a full atom representation. At each step of the procedure, an all-atom model of the protein is built using the template protein structure and the current designed sequence. The energy of the model is used to drive a Monte Carlo optimization in sequence space: random moves are either accepted or rejected based on the Metropolis criterion. We rely on the physical forces that stabilize native protein structures to choose the optimum sequence. Our energy function includes van der Waals interactions, electrostatics and an environment free energy. Successful protein design should be specific and generate a sequence compatible with the template fold and incompatible with competing folds. We impose specificity by maintaining the amino acid composition constant, based on the random energy model. The specificity of the optimized sequence is tested by fold recognition 
techniques. Successful sequence designs for the B1 domain of protein G, for the lambda repressor and for sperm whale myoglobin are presented. We show that each additional term of the energy function improves the performance of our design procedure: the van der Waals term ensures correct packing, the electrostatics term increases the specificity for the correct native fold, and the environment solvation term ensures a correct pattern of buried hydrophobic and exposed hydrophilic residues. For the globin family, we show that we can design a protein sequence that is stable in the myoglobin fold, yet incompatible with the very similar hemoglobin fold.},
  Institution              = {Department of Structural Biology, Fairchild Building, Stanford University, Stanford, CA 94305, USA. koehl@hyper.stanford.edu},
  Keywords                 = {Amino Acid Sequence; Bacterial Proteins, chemistry/genetics/metabolism; DNA-Binding Proteins; Databases, Factual; Drug Stability; Hemoglobins, chemistry/metabolism; Models, Molecular; Molecular Sequence Data; Monte Carlo Method; Mutation; Myoglobin, chemistry/metabolism; Protein Engineering, methods; Protein Folding; Protein Structure, Secondary; Proteins, chemistry/metabolism; Repressor Proteins, chemistry/genetics/metabolism; Sequence Alignment; Software; Solvents; Static Electricity; Structure-Activity Relationship; Substrate Specificity; Thermodynamics; Viral Proteins; Viral Regulatory and Accessory Proteins},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(99)93211-4},
  Pmid                     = {10547293},
  Timestamp                = {2010.09.22}
}

@Article{Kondo2002,
  Title                    = {Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect.},
  Author                   = {Kondo, Natsuko and Nikoh, Naruo and Ijichi, Nobuyuki and Shimada, Masakazu and Fukatsu, Takema},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2002},

  Month                    = {Oct},
  Number                   = {22},
  Pages                    = {14280--14285},
  Volume                   = {99},

  Abstract                 = {The adzuki bean beetle, Callosobruchus chinensis, is triple-infected with distinct lineages of Wolbachia endosymbiont, wBruCon, wBruOri, and wBruAus, which were identified by their wsp (Wolbachia surface protein) gene sequences. Whereas wBruCon and wBruOri caused cytoplasmic incompatibility of the host insect, wBruAus did not. Although wBruCon and wBruOri were easily eliminated by antibiotic treatments, wBruAus persisted over five treated generations and could not be eliminated. The inheritance pattern of wBruAus was, surprisingly, explained by sex-linked inheritance in male-heterozygotic organisms, which agreed with the karyotype of C. chinensis (2n = 20, XY). Quantitative PCR analysis demonstrated that females contain around twice as much wsp titer as males, which is concordant with an X chromosome linkage. Specific PCR and Southern blot analyses indicated that the wBruAus-bearing strain of C. chinensis contains only a fraction of the Wolbachia gene repertoire. Several genome 
fragments of wBruAus were isolated using an inverse PCR technique. The fragments exhibited a bacterial genome structure containing a number of ORFs typical of the alpha-proteobacteria, although some of the ORFs contained disruptive mutations. In the flanking region of ftsZ gene, a non-long terminal repeat (non-LTR) retrotransposon sequence, which is typical of insects but not found from bacteria, was present. These results strongly suggest that wBruAus has no microbial entity but is a genome fragment of Wolbachia endosymbiont transferred to the X chromosome of the host insect.},
  Institution              = {Department of Systems Science (Biology), and Department of Biological Science at the Graduate School of Arts and Sciences, University of Tokyo, Meguro, Tokyo 153-8902, Japan. t-fukatsu@aist.go.jp},
  Keywords                 = {Animals; Base Sequence; Beetles, genetics; Blotting, Southern, methods; DNA, Bacterial; Drosophila melanogaster, microbiology; Drug Resistance, Bacterial; Evolution, Molecular; Female; Gene Transfer, Horizontal; Genes, Bacterial; Genome, Bacterial; Male; Molecular Sequence Data; Polymerase Chain Reaction, methods; Rifampin, pharmacology; Symbiosis; Tetracycline, pharmacology; Wolbachia, drug effects/genetics/isolation /&/ purification; X Chromosome},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {222228199},
  Pmid                     = {12386340},
  Timestamp                = {2012.09.10}
}

@Article{Konrat2014,
  Title                    = {NMR contributions to structural dynamics studies of intrinsically disordered proteins},
  Author                   = {Konrat, Robert},
  Journal                  = {Journal of Magnetic Resonance},
  Year                     = {2014},
  Pages                    = {74--85},
  Volume                   = {241},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2015.09.17}
}

@Article{Koonin2009,
  Title                    = {Darwinian evolution in the light of genomics},
  Author                   = {Koonin, Eugene V},
  Journal                  = {Nucleic acids research},
  Year                     = {2009},
  Number                   = {4},
  Pages                    = {1011--1034},
  Volume                   = {37},

  Owner                    = {ranjan},
  Publisher                = {Oxford Univ Press},
  Timestamp                = {2015.06.24}
}

@Article{Koonin2005,
  Title                    = {Orthologs, paralogs, and evolutionary genomics.},
  Author                   = {Eugene V Koonin},
  Journal                  = {Annu Rev Genet},
  Year                     = {2005},
  Pages                    = {309--338},
  Volume                   = {39},

  Abstract                 = {Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A clear distinction between orthologs and paralogs is critical for the construction of a robust evolutionary classification of genes and reliable functional annotation of newly sequenced genomes. Genome comparisons show that orthologous relationships with genes from taxonomically distant species can be established for the majority of the genes from each sequenced genome. This review examines in depth the definitions and subtypes of orthologs and paralogs, outlines the principal methodological approaches employed for identification of orthology and paralogy, and considers evolutionary and functional implications of these concepts.},
  Institution              = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA. koonin@ncbi.nlm.nih.gov},
  Keywords                 = {Animals; Computational Biology; Conserved Sequence; Evolution, Molecular; Genomics},
  Owner                    = {ranjan},
  Pmid                     = {16285863},
  Timestamp                = {2011.05.12}
}

@Article{Koonin2000,
  Title                    = {The impact of comparative genomics on our understanding of evolution.},
  Author                   = {E. V. Koonin and L. Aravind and A. S. Kondrashov},
  Journal                  = {Cell},
  Year                     = {2000},

  Month                    = {Jun},
  Number                   = {6},
  Pages                    = {573--576},
  Volume                   = {101},

  Institution              = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA. koonin@ncbi.nlm.nih.gov},
  Keywords                 = {Animals; Evolution; Evolution, Molecular; Genome; Humans},
  Owner                    = {ranjan},
  Pii                      = {S0092-8674(00)80867-3},
  Pmid                     = {10892642},
  Timestamp                = {2010.05.19}
}

@Article{Korb2011,
  Title                    = {Evolution unbound: releasing the arrow of complexity},
  Author                   = {Kevin B. Korb and Alan Dorin},
  Journal                  = {Biol Philos},
  Year                     = {2011},
  Pages                    = {317-338},
  Volume                   = {26},

  File                     = {:/home/ranjan/research/jabref/pdfs/Korb2011.pdf:PDF},
  Owner                    = {ranjan},
  Timestamp                = {2011.08.07}
}

@Article{KoshlandJr1958,
  Title                    = {Application of a theory of enzyme specificity to protein synthesis},
  Author                   = {Koshland Jr, DE},
  Journal                  = {Proceedings of the National Academy of Sciences of the United States of America},
  Year                     = {1958},
  Number                   = {2},
  Pages                    = {98},
  Volume                   = {44},

  Owner                    = {ranjan},
  Publisher                = {National Academy of Sciences},
  Timestamp                = {2013.07.20}
}

@Article{Koshland2004,
  Title                    = {Crazy, but correct},
  Author                   = {Koshland, Daniel E},
  Journal                  = {Nature},
  Year                     = {2004},
  Number                   = {7016},
  Pages                    = {447--447},
  Volume                   = {432},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2013.07.20}
}

@Article{Kosol2013,
  Title                    = {Structural characterization of intrinsically disordered proteins by NMR spectroscopy},
  Author                   = {Kosol, Simone and Contreras-Martos, Sara and Cede{\~n}o, Cesyen and Tompa, Peter},
  Journal                  = {Molecules},
  Year                     = {2013},
  Number                   = {9},
  Pages                    = {10802--10828},
  Volume                   = {18},

  Owner                    = {ranjan},
  Publisher                = {Multidisciplinary Digital Publishing Institute},
  Timestamp                = {2015.09.17}
}

@Article{Krakauer2002,
  Title                    = {Noisy clues to the origin of life.},
  Author                   = {Krakauer, David C. and Sasaki, Akira},
  Journal                  = {Proc Biol Sci},
  Year                     = {2002},

  Month                    = {Dec},
  Number                   = {1508},
  Pages                    = {2423--2428},
  Volume                   = {269},

  Abstract                 = {The origin of stable self-replicating molecules represents a fundamental obstacle to the origin of life. The low fidelity of primordial replicators places restrictions on the quantity of information encoded in a primitive nucleic acid alphabet. Further difficulties for the origin of life are the role of drift in small primordial populations, reducing the rate of fixation of superior replicators, and the hostile conditions increasing developmental noise. Thus, mutation, noise and drift are three different stochastic effects that are assumed to make the evolution of life improbable. Here we show, to the contrary, how noise present in hostile early environments can increase the probability of faithful replication, by amplifying selection in finite populations. Noise has negative consequences in infinite populations, whereas in finite populations, we observe a synergistic interaction among noise sources. Hence, two factors formerly considered inimical to the origin of life-
developmental noise and drift in small populations-can in combination give rise to conditions favourable to robust replication.},
  Institution              = {Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA. krakauer@santafe.edu},
  Keywords                 = {Biogenesis; Biological Evolution; Catalysis; Genetic Drift; Models, Biological; Mutation; Nucleic Acids, metabolism; Proteins, metabolism; Stochastic Processes},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {12495484},
  Timestamp                = {2012.04.05}
}

@Article{Kudirka2011,
  Title                    = {Folding of a single-chain, information-rich polypeptoid sequence into a highly ordered nanosheet.},
  Author                   = {Kudirka, Romas and Tran, Helen and Sanii, Babak and Nam, Ki Tae and Choi, Philip H. and Venkateswaran, Neeraja and Chen, Ritchie and Whitelam, Stephen and Zuckermann, Ronald N.},
  Journal                  = {Biopolymers},
  Year                     = {2011},
  Number                   = {5},
  Pages                    = {586--595},
  Volume                   = {96},

  Abstract                 = {The design and synthesis of protein-like polymers is a fundamental challenge in materials science. A means to achieve this goal is to create synthetic polymers of defined sequence where all relevant folding information is incorporated into a single polymer strand. We present here the aqueous self-assembly of peptoid polymers (N-substituted glycines) into ultrathin, two-dimensional highly ordered nanosheets, where all folding information is encoded into a single chain. The sequence designs enforce a two-fold amphiphilic periodicity. Two sequences were considered: one with charged residues alternately positive and negative (alternating patterning), and one with charges segregated in positive and negative halves of the molecule (block patterning). Sheets form between pH 5 and 10 with the optimal conditions being pH 6 for the alternating sequence and pH 8 for the block sequence. Once assembled, the nanosheets remain stable between pH 6 and 10 with observed degradation beginning to 
occur below pH 6. The alternating charge nanosheets remain stable up to concentrations of 20\% acetonitrile, whereas the block pattern displayed greater robustness remaining stable up to 30\% acetonitrile. These observations are consistent with expectations based on considerations of the molecules' electrostatic interactions. This study represents an important step in the construction of abiotic materials founded on biological informatic and folding principles.},
  Institution              = {The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.},
  Keywords                 = {Acetonitriles, chemistry; Computer Simulation; Hydrogen-Ion Concentration; Microscopy, Electron, Scanning; Molecular Structure; Nanotechnology; Peptidomimetics; Peptoids, chemistry; Protein Folding; Protein Structure, Secondary; Static Electricity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {22180906},
  Timestamp                = {2014.05.10}
}

@Article{Kumar2005,
  Title                    = {Molecular clocks: four decades of evolution.},
  Author                   = {Sudhir Kumar},
  Journal                  = {Nat Rev Genet},
  Year                     = {2005},

  Month                    = {Aug},
  Number                   = {8},
  Pages                    = {654--662},
  Volume                   = {6},

  Abstract                 = {During the past four decades, the molecular-clock hypothesis has provided an invaluable tool for building evolutionary timescales, and has served as a null model for testing evolutionary and mutation rates in different species. Molecular clocks have also influenced the development of theories of molecular evolution. As DNA-sequencing technologies have progressed, the use of molecular clocks has increased, with a profound effect on our understanding of the temporal diversification of species and genomes.},
  Institution              = {Center for Evolutionary Functional Genomics, The Biodesign Institute and School of Life Sciences, Arizona State University, Tempe 85287-5301, USA. s.kumar@asu.edu},
  Keywords                 = {Animals; Evolution, Molecular; Humans; Proteins, genetics},
  Owner                    = {ranjan},
  Pmid                     = {16136655},
  Timestamp                = {2010.12.17}
}

@Article{Kuppler2009,
  Title                    = {Potential applications of metal-organic frameworks},
  Author                   = {Kuppler, Ryan J and Timmons, Daren J and Fang, Qian-Rong and Li, Jian-Rong and Makal, Trevor A and Young, Mark D and Yuan, Daqiang and Zhao, Dan and Zhuang, Wenjuan and Zhou, Hong-Cai},
  Journal                  = {Coordination Chemistry Reviews},
  Year                     = {2009},
  Number                   = {23},
  Pages                    = {3042--3066},
  Volume                   = {253},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2015.03.22}
}

@Article{Kurland2003,
  Title                    = {Horizontal gene transfer: a critical view.},
  Author                   = {C. G. Kurland and B. Canback and Otto G Berg},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2003},

  Month                    = {Aug},
  Number                   = {17},
  Pages                    = {9658--9662},
  Volume                   = {100},

  Abstract                 = {It has been suggested that horizontal gene transfer (HGT) is the "essence of phylogeny." In contrast, much data suggest that this is an exaggeration resulting in part from a reliance on inadequate methods to identify HGT events. In addition, the assumption that HGT is a ubiquitous influence throughout evolution is questionable. Instead, rampant global HGT is likely to have been relevant only to primitive genomes. In modern organisms we suggest that both the range and frequencies of HGT are constrained most often by selective barriers. As a consequence those HGT events that do occur most often have little influence on genome phylogeny. Although HGT does occur with important evolutionary consequences, classical Darwinian lineages seem to be the dominant mode of evolution for modern organisms.},
  File                     = {Kurland2003.pdf:pdfs/Kurland2003.pdf:PDF},
  Institution              = {Department of Molecular Evolution, Evolutionary Biology Centre, University of Uppsala, S-75236 Uppsala, Sweden.},
  Keywords                 = {Animals; Archaea, genetics; Bacteria, genetics; Evolution; Gene Transfer, Horizontal; Genome; Humans; Models, Genetic; Phylogeny; RNA, Ribosomal, genetics},
  Owner                    = {ranjan},
  Pii                      = {1632870100},
  Pmid                     = {12902542},
  Timestamp                = {2010.05.20}
}

@Article{Kuser2008,
  Title                    = {Crystal structure of yeast hexokinase PI in complex with glucose: a classical ``induced fit'' example revised},
  Author                   = {Kuser, Paula and Cupri, Fabio and Bleicher, Lucas and Polikarpov, Igor},
  Journal                  = {Proteins: Structure, Function, and Bioinformatics},
  Year                     = {2008},
  Number                   = {2},
  Pages                    = {731--740},
  Volume                   = {72},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2013.11.17}
}

@Article{Kyte1982,
  Title                    = {A simple method for displaying the hydropathic character of a protein.},
  Author                   = {J. Kyte and R. F. Doolittle},
  Journal                  = {J Mol Biol},
  Year                     = {1982},

  Month                    = {May},
  Number                   = {1},
  Pages                    = {105--132},
  Volume                   = {157},

  Keywords                 = {Amino Acid Sequence; Amino Acids, analysis; Animals; Bacteriorhodopsins; Chymotrypsinogen; L-Lactate Dehydrogenase; Membrane Proteins; Methods; Proteins, analysis; Water},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {0022-2836(82)90515-0},
  Pmid                     = {7108955},
  Timestamp                = {2013.05.06}
}

@Article{Lacy2004,
  Title                    = {p27 binds cyclin-CDK complexes through a sequential mechanism involving binding-induced protein folding.},
  Author                   = {Lacy, Eilyn R. and Filippov, Igor and Lewis, William S. and Otieno, Steve and Xiao, Limin and Weiss, Sonja and Hengst, Ludger and Kriwacki, Richard W.},
  Journal                  = {Nat Struct Mol Biol},
  Year                     = {2004},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {358--364},
  Volume                   = {11},

  Abstract                 = {p27 controls cell proliferation by binding and regulating nuclear cyclin-dependent kinases (CDKs). In addition, p27 interacts with other nuclear and cytoplasmic targets and has diverse biological functions. We seek to understand how the structural and dynamic properties of p27 mediate its several functions. We show that, despite showing disorder before binding its targets, p27 has nascent secondary structure that may have a function in molecular recognition. Binding to Cdk2-cyclin A is accompanied by p27 folding, and kinetic data suggest a sequential mechanism that is initiated by binding to cyclin A. p27 regulates CDK-cyclin complexes involved directly in cell cycle control and does not interact with other closely related CDKs. We show that p27-cyclin interactions are an important determinant of this specificity and propose that the homologous cell cycle regulators p21 and p57 function by a similar sequential, folding-on-binding mechanism.},
  Doi                      = {10.1038/nsmb746},
  Institution              = {Department of Structural Biology, St. Jude Children's Research Hospital, 332, North Lauderdale Street, Memphis, Tennessee 38105, USA.},
  Keywords                 = {Amino Acid Sequence; CDC2-CDC28 Kinases, chemistry/metabolism; Conserved Sequence; Cyclin-Dependent Kinase 2; Cyclins, chemistry/metabolism; Humans; Kinetics; Magnetic Resonance Spectroscopy; Microfilament Proteins, chemistry/metabolism; Models, Molecular; Molecular Sequence Data; Muscle Proteins; Protein Conformation; Protein Folding; Sequence Alignment; Sequence Homology, Amino Acid; Solutions; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nsmb746},
  Pmid                     = {15024385},
  Timestamp                = {2013.12.12}
}

@Article{Lagunas1970,
  Title                    = {Induced fit in yeast hexokinase},
  Author                   = {Lagunas, Rosario and Sols, Alberto and others},
  Journal                  = {European Journal of Biochemistry},
  Year                     = {1970},
  Number                   = {2},
  Pages                    = {226--233},
  Volume                   = {16},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2013.11.18}
}

@Article{Laity2001,
  Title                    = {Zinc finger proteins: new insights into structural and functional diversity},
  Author                   = {Laity, John H and Lee, Brian M and Wright, Peter E},
  Journal                  = {Current opinion in structural biology},
  Year                     = {2001},
  Number                   = {1},
  Pages                    = {39--46},
  Volume                   = {11},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.17}
}

@Other{Lambert2005,
  Title                    = {Entropy is simple -- If we avoid the briar patches},
  Author                   = {Lambert, FL},
  Month                    = aug,
  Url                      = {http://entropysimple.oxy.edu/content.htm},
  Year                     = {2013}
}

@Book{Landsteiner1936,
  Title                    = {The specificity of serological reactions},
  Author                   = {Landsteiner, Karl},
  Publisher                = {Dover Publications (reprinted 1962)},
  Year                     = {1936},

  Address                  = {Mineola, NY},

  Owner                    = {ranjan},
  Timestamp                = {2013.06.30}
}

@Article{Lanfear2011,
  Title                    = {Reply to Englund: Molecular evolution and diversification--Counting species is better than counting nodes when the phylogeny is unknown},
  Author                   = {Robert Lanfear and Lindell Bromham and Simon Y. W. Ho},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2011},
  Number                   = {17},
  Pages                    = {E85-E86},
  Volume                   = {108},

  Owner                    = {ranjan},
  Timestamp                = {2011.04.27}
}

@Article{Lanfear2010,
  Title                    = {Mutation rate is linked to diversification in birds.},
  Author                   = {Robert Lanfear and Simon Y W Ho and Dominic Love and Lindell Bromham},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2010},

  Month                    = {Nov},
  Number                   = {47},
  Pages                    = {20423--20428},
  Volume                   = {107},

  Abstract                 = {How does genome evolution affect the rate of diversification of biological lineages? Recent studies have suggested that the overall rate of genome evolution is correlated with the rate of diversification. If true, this claim has important consequences for understanding the process of diversification, and implications for the use of DNA sequence data to reconstruct evolutionary history. However, the generality and cause of this relationship have not been established. Here, we test the relationship between the rate of molecular evolution and net diversification with a 19-gene, 17-kb DNA sequence dataset from 64 families of birds. We show that rates of molecular evolution are positively correlated to net diversification in birds. Using a 7.6-kb dataset of protein-coding DNA, we show that the synonymous substitution rate, and therefore the mutation rate, is correlated to net diversification. Further analysis shows that the link between mutation rates and net diversification is 
unlikely to be the indirect result of correlations with life-history variables that may influence both quantities, suggesting that there might be a causal link between mutation rates and net diversification.},
  Institution              = {Centre for Macroevolution and Macroecology, Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra ACT 0200, Australia. rob.lanfear@anu.edu.au},
  Keywords                 = {Age Factors; Animals; Base Sequence; Biodiversity; Birds, genetics; Body Size; Computational Biology; Evolution, Molecular; Genetic Speciation; Linear Models; Mutation, genetics; Phylogeny; Population Density; Sequence Alignment; Sex Characteristics},
  Owner                    = {ranjan},
  Pii                      = {1007888107},
  Pmid                     = {21059910},
  Timestamp                = {2011.04.26}
}

@Article{Lanfear2010a,
  Title                    = {Watching the clock: studying variation in rates of molecular evolution between species.},
  Author                   = {Robert Lanfear and John J Welch and Lindell Bromham},
  Journal                  = {Trends Ecol Evol},
  Year                     = {2010},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {495--503},
  Volume                   = {25},

  Abstract                 = {Evidence is accumulating that rates of molecular evolution vary substantially between species, and that this rate variation is partly determined by species characteristics. A better understanding of how and why rates of molecular evolution vary provides a window on evolutionary processes, and might facilitate improvements in DNA sequence analysis. Measuring rates of molecular evolution and identifying the correlates of rate variation present a unique set of challenges. We describe and compare recent methodological advances that have been proposed to deal with these challenges. We provide a guide to the theoretical basis and practical application of the methods, outline the types of data on which they can be used, and indicate the types of questions they can be used to ask.},
  Institution              = {Centre for Macroevolution and Macroecology, Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra ACT 0200, Australia. rob.lanfear@anu.edu.au},
  Keywords                 = {Animals; Evolution, Molecular; Genetic Speciation; Genetic Variation; Models, Genetic; Time Factors},
  Owner                    = {ranjan},
  Pii                      = {S0169-5347(10)00146-1},
  Pmid                     = {20655615},
  Timestamp                = {2011.04.26}
}

@Article{Lange2008,
  Title                    = {Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.},
  Author                   = {Oliver F Lange and Nils-Alexander Lakomek and Christophe Far\`{e}s and Gunnar F Schr\"{o}der and Korvin F A Walter and Stefan Becker and Jens Meiler and Helmut Grubm\"{u}ller and Christian Griesinger and Bert L de Groot},
  Journal                  = {Science},
  Year                     = {2008},

  Month                    = {Jun},
  Number                   = {5882},
  Pages                    = {1471--1475},
  Volume                   = {320},

  Abstract                 = {Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.},
  Institution              = {Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 G?ttingen, Germany.},
  Keywords                 = {Amino Acid Motifs; Animals; Anisotropy; Chemistry, Physical; Crystallography, X-Ray; Entropy; Kinetics; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Physicochemical Phenomena; Protein Binding; Protein Conformation; Protein Structure, Tertiary; Solutions; Ubiquitin, chemistry/metabolism; Xenopus laevis},
  Owner                    = {ranjan},
  Pii                      = {320/5882/1471},
  Pmid                     = {18556554},
  Timestamp                = {2010.02.05}
}

@Article{Langford2001,
  Title                    = {Is the Property Being Positively of Correlated Transitive?},
  Author                   = {Langford, E. and Schwertman, N. and Owens, M.},
  Journal                  = {The American Statistician},
  Year                     = {2001},
  Pages                    = {322-325},
  Volume                   = {55},

  Owner                    = {ranjan},
  Timestamp                = {2012.09.29}
}

@Article{Larson2005,
  Title                    = {Crystallographic structure of the T=1 particle of brome mosaic virus.},
  Author                   = {Larson, S.B. and Lucas, R.W. and McPherson, A.g},
  Journal                  = JMB,
  Year                     = {2005},
  Number                   = {3},
  Pages                    = {815-831},
  Volume                   = {346},

  File                     = {Larson2005.pdf:pdfs/Larson2005.pdf:PDF}
}

@Article{Laskowski2003,
  Title                    = {Structural quality assurance},
  Author                   = {Laskowski, Roman A},
  Journal                  = {Structural Bioinformatics, Volume 44},
  Year                     = {2003},
  Pages                    = {273--303},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2015.09.09}
}

@Article{Laskowski1993,
  Title                    = {PROCHECK: a program to check the stereochemical quality of protein structures},
  Author                   = {Laskowski, Roman A and MacArthur, Malcolm W and Moss, David S and Thornton, Janet M},
  Journal                  = {Journal of applied crystallography},
  Year                     = {1993},
  Number                   = {2},
  Pages                    = {283--291},
  Volume                   = {26},

  Owner                    = {ranjan},
  Publisher                = {International Union of Crystallography},
  Timestamp                = {2015.09.08}
}

@Article{Laudet1997,
  Title                    = {Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor.},
  Author                   = {V. Laudet},
  Journal                  = {J Mol Endocrinol},
  Year                     = {1997},

  Month                    = {Dec},
  Number                   = {3},
  Pages                    = {207--226},
  Volume                   = {19},

  Abstract                 = {From a database containing the published nuclear hormone receptor (NR) sequences I constructed an alignment of the C, D and E domains of these molecules. Using this alignment, I have performed tree reconstruction using both distance matrix and parsimony analysis. The robustness of each branch was estimated using bootstrap resampling methods. The trees constructed by these two methods gave congruent topologies. From these analyses I defined six NR subfamilies: (i) a large one clustering thyroid hormone receptors (TRs), retinoic acid receptors (RARs), peroxisome proliferator-activated receptors (PPARs), vitamin D receptors (VDRs) and ecdysone receptors (EcRs) as well as numerous orphan receptors such as RORs or Rev-erbs; (ii) one containing retinoid X receptors (RXRs) together with COUP, HNF4, tailless, TR2 and TR4 orphan receptors; (iii) one containing steroid receptors; (iv) one containing the NGFIB orphan receptors; (v) one containing FTZ-F1 orphan receptors; and finally (vi) 
one containing to date only one gene, the GCNF1 orphan receptor. The relationships between the six subfamilies are not known except for subfamilies I and IV which appear to be related. Interestingly, most of the liganded receptors appear to be derived when compared with orphan receptors. This suggests that the ligand-binding ability of NRs has been gained by orphan receptors during the course of evolution to give rise to the presently known receptors. The distribution into six subfamilies correlates with the known abilities of the various NRs to bind to DNA as homo- or heterodimers. For example, receptors heterodimerizing efficiently with RXR belong to the first or the fourth subfamilies. I suggest that the ability to heterodimerize evolved once, just before the separation of subfamilies I and IV and that the first NR was able to bind to DNA as a homodimer. From the study of NR sequences existing in vertebrates, arthropods and nematodes, I define two major steps of NR diversification: one that took place 
very early, probably during the multicellularization event leading to all the metazoan phyla, and a second occurring later on, corresponding to the advent of vertebrates. Finally, I show that in vertebrate species the various groups of NRs accumulated mutations at very different rates.},
  Institution              = {URA1160 du CNRS Oncologie Mol?culaire, Institut de Biologie de Lille, Institut Pasteur de Lille, France.},
  Keywords                 = {Animals; Databases as Topic; Evolution, Molecular; Genetic Variation, genetics; Humans; Multigene Family, genetics; Mutation, genetics; Phylogeny; Protein Structure, Tertiary; Receptors, Cytoplasmic and Nuclear, chemistry/classification/genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9460643},
  Timestamp                = {2011.09.15}
}

@Article{Laursen2013,
  Title                    = {Cis--trans amide bond rotamers in $\beta$-peptoids and peptoids: evaluation of stereoelectronic effects in backbone and side chains},
  Author                   = {Laursen, Jonas S and Engel-Andreasen, Jens and Fristrup, Peter and Harris, Pernille and Olsen, Christian A},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {2013},
  Number                   = {7},
  Pages                    = {2835--2844},
  Volume                   = {135},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2014.06.11}
}

@Article{Lautru2004,
  Title                    = {Substrate recognition by nonribosomal peptide synthetase multi-enzymes.},
  Author                   = {Lautru, Sylvie and Challis, Gregory L.},
  Journal                  = {Microbiology},
  Year                     = {2004},

  Month                    = {Jun},
  Number                   = {Pt 6},
  Pages                    = {1629--1636},
  Volume                   = {150},

  Abstract                 = {Nonribosomal peptide synthetases (NRPSs) are giant multi-domain enzymes that catalyse the biosynthesis of many commercially important peptides produced by bacteria and fungi. Several studies over the last decade have shown that many of the individual domains within NRPSs exhibit significant substrate selectivity, which impacts on our ability to engineer NRPSs to produce new bioactive microbial peptides. Adenylation domains appear to be the primary determinants of substrate selectivity in NRPSs. Much progress has been made towards an empirical understanding of substrate selection by these domains over the last 5 years, but the molecular basis of substrate selectivity in these domains is not yet well understood. Perhaps surprisingly, condensation domains have also been reported to exhibit moderate to high substrate selectivity, although the generality of this observation and its potential impact on engineered biosynthesis experiments has yet to be fully elucidated. The situation 
is less clear for the thioesterase domains, which seem in certain cases to be dedicated to the hydrolysis/cyclization of their natural substrate, whereas in other cases they are largely permissive.},
  Institution              = {Department of Chemistry, The University of Warwick, Coventry CV4 7AL, UK. S.Lautru@warwick.ac.uk},
  Keywords                 = {Models, Molecular; Peptide Synthases, chemistry/genetics/metabolism; Substrate Specificity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {150/6/1629},
  Pmid                     = {15184549},
  Timestamp                = {2012.04.06}
}

@Article{Lawrence2003,
  Title                    = {Lateral gene transfer: when will adolescence end?},
  Author                   = {Lawrence, Jeffrey G. and Hendrickson, Heather},
  Journal                  = {Mol Microbiol},
  Year                     = {2003},

  Month                    = {Nov},
  Number                   = {3},
  Pages                    = {739--749},
  Volume                   = {50},

  Abstract                 = {The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fuelled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints probably stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the 
integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Here, we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.},
  Institution              = {Pittsburgh Bacteriophage Institute and Department of Biological Sciences, 352 Crawford Hall, University of Pittsburgh, Pittsburgh, PA 15260, USA. jlawrenc@pitt.edu},
  Keywords                 = {Archaea, genetics; Bacteria, genetics; Evolution, Molecular; Gene Transfer, Horizontal, physiology; Genome, Bacterial; Phylogeny; RNA, Ribosomal, genetics/physiology; Ribosomal Proteins, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {3778},
  Pmid                     = {14617137},
  Timestamp                = {2012.09.07}
}

@Article{Lawrence1998,
  Title                    = {Molecular archaeology of the Escherichia coli genome.},
  Author                   = {Lawrence, J. G. and Ochman, H.},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1998},

  Month                    = {Aug},
  Number                   = {16},
  Pages                    = {9413--9417},
  Volume                   = {95},

  Abstract                 = {The availability of the complete sequence of Escherichia coli strain MG1655 provides the first opportunity to assess the overall impact of horizontal genetic transfer on the evolution of bacterial genomes. We found that 755 of 4,288 ORFs (547.8 kb) have been introduced into the E. coli genome in at least 234 lateral transfer events since this species diverged from the Salmonella lineage 100 million years (Myr) ago. The average age of introduced genes was 14.4 Myr, yielding a rate of transfer 16 kb/Myr/lineage since divergence. Although most of the acquired genes subsequently were deleted, the sequences that have persisted ( approximately 18\% of the current chromosome) have conferred properties permitting E. coli to explore otherwise unreachable ecological niches.},
  Institution              = {Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.},
  Keywords                 = {Chromosomes, Bacterial; Escherichia coli, genetics; Evolution, Molecular; Gene Transfer, Horizontal; Genome, Bacterial},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9689094},
  Timestamp                = {2012.09.09}
}

@Article{Lazcano1996,
  Title                    = {The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time.},
  Author                   = {Lazcano, A. and Miller, S. L.},
  Journal                  = {Cell},
  Year                     = {1996},

  Month                    = {Jun},
  Number                   = {6},
  Pages                    = {793--798},
  Volume                   = {85},

  Institution              = {U CA San Diego, La Jolla},
  Keywords                 = {Atmosphere; Bacteria; Biogenesis; Biological Evolution; Evolution, Molecular; Geological Phenomena; Geology; Multigene Family; RNA; Time},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0092-8674(00)81263-5},
  Pmid                     = {8681375},
  Timestamp                = {2012.04.05}
}

@Article{Lazcano1994,
  Title                    = {How long did it take for life to begin and evolve to cyanobacteria?},
  Author                   = {Lazcano, A. and Miller, S. L.},
  Journal                  = {J Mol Evol},
  Year                     = {1994},

  Month                    = {Dec},
  Number                   = {6},
  Pages                    = {546--554},
  Volume                   = {39},

  Abstract                 = {There is convincing paleontological evidence showing that stromatolite-building phototactic prokaryotes were already in existence 3.5 x 10(9) years ago. Late accretion impacts may have killed off life on our planet as late as 3.8 x 10(9) years ago. This leaves only 300 million years to go from the prebiotic soup to the RNA world and to cyanobacteria. However, 300 million years should be more than sufficient time. All known prebiotic reactions take place in geologically rapid time scales, and very slow prebiotic reactions are not feasible because the intermediate compounds would have been destroyed due to the passage of the entire ocean through deep-sea vents every 10(7) years or in even less time. Therefore, it is likely that self-replicating systems capable of undergoing Darwinian evolution emerged in a period shorter than the destruction rates of its components (<5 million years). The time for evolution from the first DNA/protein organisms to cyanobacteria is usually thought 
to be very long. However, the similarities of many enzymatic reactions, together with the analysis of the available sequence data, suggest that a significant number of the components involved in basic biological processes are the result of ancient gene duplication events. Assuming that the rate of gene duplication of ancient prokaryotes was comparable to today's present values, the development of a filamentous cyanobacterial-like genome would require approximately 7 x 10(6) years--or perhaps much less. Thus, in spite of the many uncertainties involved in the estimates of time for life to arise and evolve to cyanobacteria, we see no compelling reason to assume that this process, from the beginning of the primitive soup to cyanobacteria, took more than 10 million years.},
  Institution              = {U CA San Diego, La Jolla},
  Keywords                 = {Biogenesis; Biological Evolution; Cyanobacteria, genetics; Evolution, Chemical; Evolution, Molecular; Multigene Family; Photosynthesis; Protein Biosynthesis; RNA, Catalytic, chemistry; RNA, chemical synthesis; Seawater; Time Factors},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {11536653},
  Timestamp                = {2012.04.06}
}

@Article{LeGall2007,
  Title                    = {Intrinsic disorder in the Protein Data Bank.},
  Author                   = {{Le Gall}, Tanguy and Romero, Pedro R. and Cortese, Marc S. and Uversky, Vladimir N. and Dunker, A Keith},
  Journal                  = {J Biomol Struct Dyn},
  Year                     = {2007},

  Month                    = {Feb},
  Number                   = {4},
  Pages                    = {325--342},
  Volume                   = {24},

  Doi                      = {10.1080/07391102.2007.10507123},
  Institution              = {Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Amino Acids, analysis; Animals; Archaeal Proteins, chemistry; Bacterial Proteins, chemistry; Databases, Protein; Models, Molecular; Protein Conformation; Proteins, chemistry; Viral Proteins, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {do=detail},
  Pmid                     = {17206849},
  Timestamp                = {2013.12.08}
}

@Book{Leach2001,
  Title                    = {Molecular Modelling: Principles and Applications},
  Author                   = {Andrew Leach},
  Publisher                = {Prentice Hall},
  Year                     = {2001},
  Edition                  = {2},

  Owner                    = {ranjan},
  Timestamp                = {2012.07.14}
}

@Article{Lee1988,
  Title                    = {Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density},
  Author                   = {Lee, Chengteh and Yang, Weitao and Parr, Robert G},
  Journal                  = {Physical Review B},
  Year                     = {1988},
  Number                   = {2},
  Pages                    = {785},
  Volume                   = {37},

  Owner                    = {ranjan},
  Publisher                = {APS},
  Timestamp                = {2014.07.23}
}

@Article{Lee2012,
  Title                    = {Structural basis for heteromeric assembly and perinuclear organization of keratin filaments},
  Author                   = {Lee, Chang-Hun and Kim, Min-Sung and Chung, Byung Min and Leahy, Daniel J and Coulombe, Pierre A},
  Journal                  = {Nature structural \& molecular biology},
  Year                     = {2012},
  Number                   = {7},
  Pages                    = {707--715},
  Volume                   = {19},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2014.06.11}
}

@Article{Lee2003,
  Title                    = {A structural perspective on genome evolution.},
  Author                   = {David Lee and Alastair Grant and Daniel Buchan and Christine Orengo},
  Journal                  = {Curr Opin Struct Biol},
  Year                     = {2003},

  Month                    = {Jun},
  Number                   = {3},
  Pages                    = {359--369},
  Volume                   = {13},

  Abstract                 = {Protein translations of over 100 complete genomes are now available. About half of these sequences can be provided with structural annotation, thereby enabling some profound insights into protein and pathway evolution. Whereas the major domain structure families are common to all kingdoms of life, these are combined in different ways in multidomain proteins to give various domain architectures that are specific to kingdoms or individual genomes, and contribute to the diverse phenotypes observed. These data argue for more targets in structural genomics initiatives and particularly for the selection of different domain architectures to gain better insights into protein functions.},
  File                     = {Lee2003.pdf:pdfs/Lee2003.pdf:PDF},
  Institution              = {Department of Biochemistry and Molecular Biology, University College, Gower Street, WC1E 6BT, London, UK. dlee@biochem.ucl.ac.uk},
  Keywords                 = {Evolution, Molecular; Genome; Phylogeny; Protein Conformation; Protein Structure, Tertiary; Species Specificity},
  Owner                    = {ranjan},
  Pii                      = {S0959440X03000794},
  Pmid                     = {12831888},
  Timestamp                = {2009.09.14}
}

@Article{Lee2000,
  Title                    = {Local structural elements in the mostly unstructured transcriptional activation domain of human p53.},
  Author                   = {Lee, H. and Mok, K. H. and Muhandiram, R. and Park, K. H. and Suk, J. E. and Kim, D. H. and Chang, J. and Sung, Y. C. and Choi, K. Y. and Han, K. H.},
  Journal                  = {J Biol Chem},
  Year                     = {2000},

  Month                    = {Sep},
  Number                   = {38},
  Pages                    = {29426--29432},
  Volume                   = {275},

  Abstract                 = {DNA transcription is initiated by a small regulatory region of transactivators known as the transactivation domain. In contrast to the rapid progress made on the functional aspect of this promiscuous domain, its structural feature is still poorly characterized. Here, our multidimensional NMR study reveals that an unbound full-length p53 transactivation domain, although similar to the recently discovered group of loosely folded proteins in that it does not have tertiary structure, is nevertheless populated by an amphipathic helix and two nascent turns. The helix is formed by residues Thr(18)-Leu(26) (Thr-Phe-Ser-Asp-Leu-Trp-Lys-Leu-Leu), whereas the two turns are formed by residues Met(40)-Met(44) and Asp(48)-Trp(53), respectively. It is remarkable that these local secondary structures are selectively formed by functionally critical and positionally conserved hydrophobic residues present in several acidic transactivation domains. This observation suggests that such local 
structures are general features of acidic transactivation domains and may represent "specificity determinants" (Ptashne, M., and Gann, A. A. F. (1997), Nature 386, 569-577) that are important for transcriptional activity.},
  Doi                      = {10.1074/jbc.M003107200},
  Institution              = {Protein Engineering Laboratory, Korea Research Institute of Bioscience and Biotechnology, Yusong, P. O. Box 115, Taejon 305-600, South Korea.},
  Keywords                 = {Amino Acid Sequence; Humans; Molecular Sequence Data; Sequence Analysis, Protein; Transcription, Genetic; Transcriptional Activation; Tumor Suppressor Protein p53, chemistry/genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {M003107200},
  Pmid                     = {10884388},
  Timestamp                = {2013.12.12}
}

@Article{Lee2001,
  Title                    = {State of the art in studying protein folding and protein structure prediction using molecular dynamics methods.},
  Author                   = {M. R. Lee and Y. Duan and P. A. Kollman},
  Journal                  = {J Mol Graph Model},
  Year                     = {2001},
  Number                   = {1},
  Pages                    = {146--149},
  Volume                   = {19},

  Abstract                 = {This study presents an overview of the state of the art in using molecular dynamics methods to simulate protein folding and in the end game of protein structure prediction. In principle, these methods should allow the highest level of detail possible and the highest accuracy, but they are limited by both the accuracy of the force field used in the simulation and the sampling possible in the available computer time. We describe current capabilities in running the simulations longer and more efficiently.},
  Institution              = {Department of Pharmaceutical Chemistry, University of CA, San Francisco, CA, USA.},
  Keywords                 = {Carrier Proteins, chemistry; Computer Simulation; Microfilament Proteins, chemistry; Protein Conformation; Protein Folding; Protein Structure, Tertiary; Proteins, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S1093-3263(00)00126-1},
  Pmid                     = {11381525},
  Timestamp                = {2011.08.03}
}

@Article{Leman2004,
  Title                    = {Carbonyl sulfide-mediated prebiotic formation of peptides.},
  Author                   = {Luke Leman and Leslie Orgel and M. Reza Ghadiri},
  Journal                  = {Science},
  Year                     = {2004},

  Month                    = {Oct},
  Number                   = {5694},
  Pages                    = {283--286},
  Volume                   = {306},

  Abstract                 = {Almost all discussions of prebiotic chemistry assume that amino acids, nucleotides, and possibly other monomers were first formed on the Earth or brought to it in comets and meteorites, and then condensed nonenzymatically to form oligomeric products. However, attempts to demonstrate plausibly prebiotic polymerization reactions have met with limited success. We show that carbonyl sulfide (COS), a simple volcanic gas, brings about the formation of peptides from amino acids under mild conditions in aqueous solution. Depending on the reaction conditions and additives used, exposure of alpha-amino acids to COS generates peptides in yields of up to 80\% in minutes to hours at room temperature.},
  Institution              = {Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.},
  Keywords                 = {Amino Acids, chemistry; Anaerobiosis; Cyclization; Dipeptides, chemistry; Evolution, Chemical; Magnetic Resonance Spectroscopy; Oligopeptides, chemistry; Oxidation-Reduction; Phenylalanine, chemistry; Serine, chemistry; Sulfur Oxides, chemistry; Temperature; Thermodynamics; Thiocarbamates, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {306/5694/283},
  Pmid                     = {15472077},
  Timestamp                = {2011.11.10}
}

@Article{Lenski1999,
  Title                    = {Genome complexity, robustness and genetic interactions in digital organisms.},
  Author                   = {R. E. Lenski and C. Ofria and T. C. Collier and C. Adami},
  Journal                  = {Nature},
  Year                     = {1999},

  Month                    = {Aug},
  Number                   = {6745},
  Pages                    = {661--664},
  Volume                   = {400},

  Abstract                 = {Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined 'metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the 
complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.},
  Institution              = {Center for Microbial Ecology, Michigan State University, East Lansing 48824, USA. lenski@pilot.msu.edu},
  Keywords                 = {Biological Evolution; Computer Simulation; Genome; Models, Genetic; Mutation; Reproduction; Software},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {10458160},
  Timestamp                = {2011.07.09}
}

@Article{Leopold1992,
  Title                    = {Protein folding funnels: a kinetic approach to the sequence-structure relationship.},
  Author                   = {Leopold, Peter E and Montal, Mauricio and Onuchic, Jos{\'e} N},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {1992},
  Number                   = {18},
  Pages                    = {8721--8725},
  Volume                   = {89},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2014.09.02}
}

@Article{Lepault2001,
  Title                    = {Structural polymorphism of the major capsid protein of rotavirus.},
  Author                   = {Lepault,J. and Petitpas,I. and Erk,I. and Navaza,J. and Bigot,D. and Dona,M. and Vachette,P. and Cohen,J. and Rey,F.A.},
  Journal                  = {EMBO J.},
  Year                     = {2001},
  Number                   = {7},
  Pages                    = {1498--1507},
  Volume                   = {20},

  File                     = {Lepault2001.pdf:pdfs/Lepault2001.pdf:PDF}
}

@Article{Lerman2007,
  Title                    = {Defining functional distance using manifold embeddings of gene ontology annotations.},
  Author                   = {Gilad Lerman and Boris E Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2007},

  Month                    = {Jul},
  Number                   = {27},
  Pages                    = {11334--11339},
  Volume                   = {104},

  Abstract                 = {Although rigorous measures of similarity for sequence and structure are now well established, the problem of defining functional relationships has been particularly daunting. Here, we present several manifold embedding techniques to compute distances between Gene Ontology (GO) functional annotations and consequently estimate functional distances between protein domains. To evaluate accuracy, we correlate the functional distance to the well established measures of sequence, structural, and phylogenetic similarities. Finally, we show that manual classification of structures into folds and superfamilies is mirrored by proximity in the newly defined function space. We show how functional distances place structure-function relationships in biological context resulting in insight into divergent and convergent evolution. The methods and results in this paper can be readily generalized and applied to a wide array of biologically relevant investigations, such as accuracy of annotation 
transference, the relationship between sequence, structure, and function, or coherence of expression modules.},
  Institution              = {Department of Mathematics, University of Minnesota, Minneapolis, MN 55455, USA. lerman@umn.edu},
  Keywords                 = {Evolution, Molecular; Models, Genetic; Protein Structure, Tertiary; Proteins, chemistry/genetics/physiology; Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid; Structure-Activity Relationship},
  Owner                    = {ranjan},
  Pii                      = {0702965104},
  Pmid                     = {17595300},
  Timestamp                = {2009.12.05}
}

@Article{Letunic2007,
  Title                    = {Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.},
  Author                   = {Ivica Letunic and Peer Bork},
  Journal                  = {Bioinformatics},
  Year                     = {2007},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {127--128},
  Volume                   = {23},

  Abstract                 = {Interactive Tree Of Life (iTOL) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. Trees can be interactively pruned and re-rooted. Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported. AVAILABILITY: iTOL is available at http://itol.embl.de},
  Institution              = {EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.},
  Keywords                 = {Algorithms; Animals; Chromosome Mapping, instrumentation/methods; Computational Biology; Data Display; Databases, Genetic; Decision Trees; Evolution, Molecular; Humans; Internet; Phylogeny; Software; Species Specificity; User-Computer Interface},
  Owner                    = {ranjan},
  Pii                      = {btl529},
  Pmid                     = {17050570},
  Timestamp                = {2010.06.23}
}

@Article{Levy2006,
  Title                    = {3D complex: a structural classification of protein complexes.},
  Author                   = {Emmanuel D Levy and Jose B Pereira-Leal and Cyrus Chothia and Sarah A Teichmann},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2006},

  Month                    = {Nov},
  Number                   = {11},
  Pages                    = {e155},
  Volume                   = {2},

  Abstract                 = {Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of 
arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.},
  Institution              = {Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom. elevy@mrc-lmb.cam.ac.uk},
  Keywords                 = {Amino Acid Sequence; Binding Sites; Computer Simulation; Databases, Protein; Models, Chemical; Models, Molecular; Molecular Sequence Data; Multiprotein Complexes, chemistry/ultrastructure; Protein Binding; Protein Conformation; Protein Interaction Mapping, methods; Proteins, chemistry/classification/ultrastructure; Sequence Analysis, Protein, methods},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {06-PLCB-RA-0245R2},
  Pmid                     = {17112313},
  Timestamp                = {2011.08.07}
}

@Article{Li1996,
  Title                    = {Emergence of preferred structures in a simple model of protein folding.},
  Author                   = {H. Li and R. Helling and C. Tang and N. Wingreen},
  Journal                  = {Science},
  Year                     = {1996},

  Month                    = {Aug},
  Number                   = {5275},
  Pages                    = {666--669},
  Volume                   = {273},

  Abstract                 = {Protein structures in nature often exhibit a high degree of regularity (for example, secondary structure and tertiary symmetries) that is absent from random compact conformations. With the use of a simple lattice model of protein folding, it was demonstrated that structural regularities are related to high "designability" and evolutionary stability. The designability of each compact structure is measured by the number of sequences that can design the structure-that is, sequences that possess the structure as their nondegenerate ground state. Compact structures differ markedly in terms of their designability; highly designable structures emerge with a number of associated sequences much larger than the average. These highly designable structures possess "proteinlike" secondary structure and even tertiary symmetries. In addition, they are thermodynamically more stable than other structures. These results suggest that protein structures are selected in nature because they are 
readily designed and stable against mutations, and that such a selection simultaneously leads to thermodynamic stability.},
  Institution              = {NEC Research Institute, 4 Independence Way, Princeton, NJ 08540, USA.},
  Keywords                 = {Amino Acid Sequence; Evolution, Molecular; Models, Molecular; Mutation; Protein Conformation; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins, chemistry/genetics; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {8662562},
  Timestamp                = {2011.10.30}
}

@Article{Li2008,
  Title                    = {The flavivirus precursor membrane-envelope protein complex: structure and maturation.},
  Author                   = {Li,L. and Lok,S.M. and Yu,I.M. and Zhang,Y. and Kuhn,R.J. and Chen,J. and Rossmann,M.G.},
  Journal                  = {Science.},
  Year                     = {2008},
  Number                   = {5871},
  Pages                    = {1830-1834},
  Volume                   = {319},

  File                     = {Li2008.pdf:pdfs/Li2008.pdf:PDF}
}

@Article{Li2000,
  Title                    = {Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus.},
  Author                   = {L. Li and L. A. Mirny and E. I. Shakhnovich},
  Journal                  = {Nat Struct Biol},
  Year                     = {2000},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {336--342},
  Volume                   = {7},

  Abstract                 = {A lattice model with side chains was used to investigate protein folding with computer simulations. In this model, we rigorously demonstrate the existence of a specific folding nucleus. This nucleus contains specific interactions not present in the native state that, when weakened, slow folding but do not change protein stability. Such a decoupling of folding kinetics from thermodynamics has been observed experimentally for real proteins. From our results, we conclude that specific non-native interactions in the transition state would give rise to straight phi-values that are negative or larger than unity. Furthermore, we demonstrate that residue Ile 34 in src SH3, which has been shown to be kinetically, but not thermodynamically, important, is universally conserved in proteins with the SH3 fold. This is a clear example of evolution optimizing the folding rate of a protein independent of its stability and function.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.},
  Keywords                 = {Amino Acid Sequence; Amino Acid Substitution; Binding Sites; Computer Simulation; Conserved Sequence; Enzyme Stability; Evolution, Molecular; Kinetics; Models, Chemical; Models, Molecular; Molecular Sequence Data; Monte Carlo Method; Mutation; Protein Folding; Proteins, chemistry/metabolism; Proto-Oncogene Proteins pp60(c-src), chemistry/metabolism; Sequence Alignment; Thermodynamics; src Homology Domains},
  Owner                    = {ranjan},
  Pmid                     = {10742180},
  Timestamp                = {2009.12.05}
}

@Article{Libersou2008,
  Title                    = {Geometric mismatches within the concentric layers of rotavirus particles: a potential regulatory switch of viral particle transcription activity},
  Author                   = {Libersou,S. and Siebert,X. and Ouldali,M. and Estrozi,L.F. and Navaza,J. and Charpilienne,A. and Garnier,P. and Poncet,D. and Lepault,J.},
  Journal                  = {J Virol.},
  Year                     = {2008},
  Number                   = {6},
  Pages                    = {2844--2852},
  Volume                   = {82},

  File                     = {Libersou2008.pdf:pdfs/Libersou2008.pdf:PDF}
}

@Article{Liddington1991,
  Title                    = {Structure of simian virus 40 at 3.8-A resolution},
  Author                   = {Liddington, R. C. and Yan, Y. and Moulai, J. and Sahli, R. and Benjamin, T. L. and Harrison, S. C.},
  Journal                  = {Nature.},
  Year                     = {1991},
  Number                   = {6351},
  Pages                    = {278-284},
  Volume                   = {354},

  File                     = {Liddington1991.pdf:pdfs/Liddington1991.pdf:PDF}
}

@Article{Lidmar2003,
  Title                    = {Virus shapes and buckling transitions in spherical shells},
  Author                   = {Lidmar,J. and Mirny,L. and Nelson,D.R.},
  Journal                  = PRE,
  Year                     = {2003},
  Number                   = {5 Pt 1},
  Pages                    = {051910},
  Volume                   = {68},

  File                     = {Lidmar2003.pdf:pdfs/Lidmar2003.pdf:PDF}
}

@Article{Lin2006,
  Title                    = {DNA Tile Based Self-Assembly: Building Complex Nanoarchitectures},
  Author                   = {Lin, Chenxiang and Liu, Yan and Rinker, Sherri and Yan, Hao},
  Journal                  = {ChemPhysChem},
  Year                     = {2006},
  Number                   = {8},
  Pages                    = {1641--1647},
  Volume                   = {7},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2015.03.22}
}

@InBook{Lin1988,
  Title                    = {Mathematics applied to deterministic problems in the natural sciences},
  Author                   = {Lin,C.C. and Segel,L.A.},
  Chapter                  = {Field Equations of Continuum Mechanics.},
  Pages                    = {490--491},
  Publisher                = {SIAM},
  Year                     = {1988},

  Address                  = {Philadelphia, USA}
}

@Article{Lin2003,
  Title                    = {Structures of picorna-like plant viruses: implications and applications.},
  Author                   = {Lin, T. and Johnson, J. E.},
  Journal                  = {Adv Virus Res.},
  Year                     = {2003},
  Pages                    = {167--239},
  Volume                   = {62}
}

@Book{Linderstrom-Lang1952,
  Title                    = {Lane Medical Lectures: proteins and enzymes},
  Author                   = {Linderstr{\o}m-Lang, Kaj U},
  Publisher                = {Stanford University Press},
  Year                     = {1952},
  Volume                   = {6},

  Owner                    = {ranjan},
  Timestamp                = {2013.11.12}
}

@Article{Lindorff-Larsen2005,
  Title                    = {Simultaneous determination of protein structure and dynamics.},
  Author                   = {Kresten Lindorff-Larsen and Robert B Best and Mark A Depristo and Christopher M Dobson and Michele Vendruscolo},
  Journal                  = {Nature},
  Year                     = {2005},

  Month                    = {Jan},
  Number                   = {7022},
  Pages                    = {128--132},
  Volume                   = {433},

  Abstract                 = {We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy--for obtaining experimental information at the atomic level about the structural and dynamical features of proteins--with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant advances in our ability to understand and utilize the structures of native 
proteins.},
  Institution              = {Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.},
  Keywords                 = {Computer Simulation; Humans; Magnetic Resonance Spectroscopy; Models, Molecular; Protein Conformation; Reproducibility of Results; Solutions, chemistry; Ubiquitin, chemistry/metabolism},
  Owner                    = {ranjan},
  Pii                      = {nature03199},
  Pmid                     = {15650731},
  Timestamp                = {2010.02.14}
}

@Article{Lipovetsky2002,
  Title                    = {Comment on ``{I}s the Property of Being Positively Correlated Transitive?''},
  Author                   = {Lipovetsky, Stan},
  Journal                  = {The American Statistician},
  Year                     = {2002},
  Number                   = {4},
  Pages                    = {pp. 341-342},
  Volume                   = {56},

  Copyright                = {Copyright ? 2002 American Statistical Association},
  ISSN                     = {00031305},
  Jstor_articletype        = {research-article},
  Jstor_formatteddate      = {Nov., 2002},
  Owner                    = {ranjan},
  Publisher                = {American Statistical Association},
  Timestamp                = {2012.09.29}
}

@Article{Liu2008,
  Title                    = {Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.},
  Author                   = {Jinfeng Liu and Yan Zhang and Xingye Lei and Zemin Zhang},
  Journal                  = {Genome Biol},
  Year                     = {2008},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {R69},
  Volume                   = {9},

  Abstract                 = {ABSTRACT: BACKGROUND: The rates of molecular evolution for protein-coding genes depend on the stringency of functional or structural constraints. The Ka/Ks ratio has been commonly used as an indicator of selective constraints and is typically calculated from interspecies alignments. Recent accumulation of single nucleotide polymorphism (SNP) data has enabled the derivation of Ka/Ks ratios for polymorphism (SNP A/S ratios). RESULTS: Using data from the dbSNP database, we conducted the first large-scale survey of SNP A/S ratios for different structural and functional properties. We confirmed that the SNP A/S ratio is largely correlated with Ka/Ks for divergence. We observed stronger selective constraints for proteins that have high mRNA expression levels or broad expression patterns, have no paralogs, arose earlier in evolution, have natively disordered regions, are located in cytoplasm and nucleus, or are related to human diseases. On the residue level, we found higher degrees of 
variation for residues that are exposed to solvent, are in a loop conformation, natively disordered regions or low complexity regions, or are in the signal peptides of secreted proteins. Our analysis also revealed that histones and protein kinases are among the protein families that are under the strongest selective constraints, whereas olfactory and taste receptors are among the most variable groups. CONCLUSION: Our study suggests that the SNP A/S ratio is a robust measure for selective constraints. The correlations between SNP A/S ratios and other variables provide valuable insights into the natural selection of various structural or functional properties, particularly for human-specific genes and constraints within the human lineage.},
  File                     = {Liu2008.pdf:pdfs/Liu2008.pdf:PDF},
  Institution              = {Department of Bioinformatics, Genentech Inc,, 1 DNA Way, South San Francisco, CA 94080, USA. zemin@gene.com.},
  Owner                    = {ranjan},
  Pii                      = {gb-2008-9-4-r69},
  Pmid                     = {18397526},
  Timestamp                = {2009.09.14}
}

@Article{Liu2006,
  Title                    = {Crystal structures of the editing domain of Escherichia coli leucyl-tRNA synthetase and its complexes with Met and Ile reveal a lock-and-key mechanism for amino acid discrimination},
  Author                   = {Liu, Yunqing and Liao, Jing and Zhu, Bin and Wang, E and Ding, Jianping},
  Journal                  = {Biochem. J},
  Year                     = {2006},
  Pages                    = {399--407},
  Volume                   = {394},

  Owner                    = {ranjan},
  Timestamp                = {2013.11.17}
}

@Article{Lobanov2010,
  Title                    = {Library of disordered patterns in 3D protein structures.},
  Author                   = {Lobanov, Michail Yu and Furletova, Eugeniya I. and Bogatyreva, Natalya S. and Roytberg, Michail A. and Galzitskaya, Oxana V.},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2010},
  Number                   = {10},
  Pages                    = {e1000958},
  Volume                   = {6},

  Abstract                 = {Intrinsically disordered regions serve as molecular recognition elements, which play an important role in the control of many cellular processes and signaling pathways. It is useful to be able to predict positions of disordered regions in protein chains. The statistical analysis of disordered residues was done considering 34,464 unique protein chains taken from the PDB database. In this database, 4.95\% of residues are disordered (i.e. invisible in X-ray structures). The statistics were obtained separately for the N- and C-termini as well as for the central part of the protein chain. It has been shown that frequencies of occurrence of disordered residues of 20 types at the termini of protein chains differ from the ones in the middle part of the protein chain. Our systematic analysis of disordered regions in PDB revealed 109 disordered patterns of different lengths. Each of them has disordered occurrences in at least five protein chains with identity less than 20\%. The vast 
majority of all occurrences of each disordered pattern are disordered. This allows one to use the library of disordered patterns for predicting the status of a residue of a given protein to be ordered or disordered. We analyzed the occurrence of the selected patterns in three eukaryotic and three bacterial proteomes.},
  Doi                      = {10.1371/journal.pcbi.1000958},
  Institution              = {Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Bacterial Proteins, chemistry; Computational Biology, methods; Databases, Protein; Eukaryota; Molecular Sequence Data; Pattern Recognition, Automated, methods; Protein Conformation; Proteins, chemistry; Proteome, chemistry; Sequence Alignment; Sequence Analysis, Protein},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pmid                     = {20976197},
  Timestamp                = {2013.12.08}
}

@Article{Lobry1997,
  Title                    = {Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species.},
  Author                   = {Lobry, J. R.},
  Journal                  = {Gene},
  Year                     = {1997},

  Month                    = {Dec},
  Number                   = {1-2},
  Pages                    = {309--316},
  Volume                   = {205},

  Abstract                 = {The amino-acid composition of 23,490 proteins from 59 bacterial species was analyzed as a function of genomic G+C content. Observed amino-acid frequencies were compared with those expected from a neutral model assuming the absence of selection on average protein composition. Integral membrane proteins and non-integral membrane proteins were analyzed separately. The average deviation from this neutral model shows that there is a selective pressure increasing content in charged amino acids for non-integral membrane proteins, and content in hydrophobic amino acids for integral membrane proteins. Amino-acid frequencies were greatly influenced by genomic G+C content, but the influence was found to be often weaker than predicted. This may be evidence for a selective pressure, maintaining most amino-acid frequencies close to an optimal value. Concordance between the genetic code and protein composition is discussed in the light of this observation.},
  Keywords                 = {Amino Acids, analysis; Bacterial Proteins, chemistry; Cytosine, analysis; Genome, Bacterial; Guanine, analysis},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9461405},
  Timestamp                = {2012.09.27}
}

@Article{Long2009,
  Title                    = {The pervasive chemistry of metal--organic frameworks},
  Author                   = {Long, Jeffrey R and Yaghi, Omar M},
  Journal                  = {Chemical Society Reviews},
  Year                     = {2009},
  Number                   = {5},
  Pages                    = {1213--1214},
  Volume                   = {38},

  Owner                    = {ranjan},
  Publisher                = {Royal Society of Chemistry},
  Timestamp                = {2015.03.22}
}

@Article{Longo2013,
  Title                    = {Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein.},
  Author                   = {Longo, Liam M. and Lee, Jihun and Blaber, Michael},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2013},

  Month                    = {Feb},
  Number                   = {6},
  Pages                    = {2135--2139},
  Volume                   = {110},

  Abstract                 = {A compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" α-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"--that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides? If so, what (if any) characteristic properties might such polypeptides exhibit? To investigate these questions, two "primitive" versions of an extant protein fold (the β-trefoil) were produced by top-down symmetric deconstruction, resulting in a reduced alphabet size of 12 or 13 amino acids and a percentage of prebiotic amino acids approaching 80\%. These proteins show a substantial acidification of pI and require high salt concentrations for cooperative folding. The results suggest that 
the prebiotic amino acids do comprise a foldable set within the halophile environment.},
  Doi                      = {10.1073/pnas.1219530110},
  Institution              = {Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306-4300, USA.},
  Keywords                 = {Amino Acids, chemistry; Biogenesis; Biophysical Phenomena; Calorimetry, Differential Scanning; Crystallography, X-Ray; Evolution, Molecular; Models, Molecular; Mutagenesis; Protein Folding; Protein Stability; Proteins, chemistry/genetics; Static Electricity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {1219530110},
  Pmid                     = {23341608},
  Timestamp                = {2014.02.25}
}

@Article{Looger2001,
  Title                    = {Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics.},
  Author                   = {L. L. Looger and H. W. Hellinga},
  Journal                  = {J Mol Biol},
  Year                     = {2001},

  Month                    = {Mar},
  Number                   = {1},
  Pages                    = {429--445},
  Volume                   = {307},

  Abstract                 = {The dead-end elimination (DEE) theorems are powerful tools for the combinatorial optimization of protein side-chain placement in protein design and homology modeling. In order to reach their full potential, the theorems must be extended to handle very hard problems. We present a suite of new algorithms within the DEE paradigm that significantly extend its range of convergence and reduce run time. As a demonstration, we show that a total protein design problem of 10(115) combinations, a hydrophobic core design problem of 10(244) combinations, and a side-chain placement problem of 10(1044) combinations are solved in less than two weeks, a day and a half, and an hour of CPU time, respectively. This extends the range of the method by approximately 53, 144 and 851 log-units, respectively, using modest computational resources. Small to average-sized protein domains can now be designed automatically, and side-chain placement calculations can be solved for nearly all sizes of proteins 
and protein complexes in the growing field of structural genomics.},
  Institution              = {Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710, USA.},
  Keywords                 = {Algorithms; Amino Acid Sequence; DNA-Binding Proteins; Fibronectins, chemistry/genetics; Genome; Humans; Immunoglobulin Fab Fragments, chemistry/genetics; Models, Chemical; Protein Conformation; Protein Engineering; Protein Folding; Repressor Proteins, chemistry/genetics; Sequence Homology, Amino Acid; Viral Proteins; Viral Regulatory and Accessory Proteins; X-Ray Diffraction},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(00)94424-3},
  Pmid                     = {11243829},
  Timestamp                = {2011.01.23}
}

@Article{Lukatsky2007,
  Title                    = {Structural similarity enhances interaction propensity of proteins.},
  Author                   = {D. B. Lukatsky and B. E. Shakhnovich and J. Mintseris and E. I. Shakhnovich},
  Journal                  = {J Mol Biol},
  Year                     = {2007},

  Month                    = {Feb},
  Number                   = {5},
  Pages                    = {1596--1606},
  Volume                   = {365},

  Abstract                 = {We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar structures. The effects originate in the fact that the probability to find a pattern self-match between two identical, even randomly organized interacting protein surfaces is always higher compared with the probability for a pattern match between two different, promiscuous protein surfaces. This theoretical finding explains statistical prevalence of homodimers in protein-protein interaction networks reported earlier. Further, our findings are confirmed by the analysis of curated database of protein complexes that showed highly statistically significant overrepresentation of dimers formed by structurally similar proteins with highly divergent sequences ("superfamily heterodimers"). We suggest that promiscuous homodimeric interactions pose strong 
competitive interactions for heterodimers evolved from homodimers. Such evolutionary bottleneck is overcome using the negative design evolutionary pressure applied against promiscuous homodimer formation. This is achieved through the formation of highly specific contacts formed by charged residues as demonstrated both in model and real superfamily heterodimers.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.},
  Keywords                 = {Amino Acids; Bacterial Proteins; DNA-Binding Proteins; Databases, Protein; Dimerization; Evolution, Molecular; Models, Molecular; Protein Binding; Proteins, chemistry/metabolism; Structural Homology, Protein; Structure-Activity Relationship},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(06)01549-X},
  Pmid                     = {17141268},
  Timestamp                = {2009.12.05}
}

@Article{Lumb1995,
  Title                    = {A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil.},
  Author                   = {K. J. Lumb and P. S. Kim},
  Journal                  = {Biochemistry},
  Year                     = {1995},

  Month                    = {Jul},
  Number                   = {27},
  Pages                    = {8642--8648},
  Volume                   = {34},

  Abstract                 = {Buried polar residues are a common feature of natural proteins. ACID-p1 and BASE-p1 are two designed peptides that form a parallel, heterodimeric coiled coil with a fixed tertiary structure [O'Shea, E. K., Lumb, K. J., & Kim, P. S. (1993) Curr. Biol. 3, 658-667]. The interface between the ACID-p1 and BASE-p1 helices consists of hydrophobic Leu residues, with the exception of a single polar residue, Asn 14. In the crystal structure of the GCN4 leucine zipper coiled coil, an analogous Asn is hydrogen bonded to the corresponding Asn of the opposing helix, thereby forming a buried polar interaction in an otherwise hydrophobic interface between the helices [O'Shea, E. K., Klemm, J. D., Kim, P. S., & Alber, T. (1991) Science 254, 539-544]. This buried polar interaction in the ACID-p1/BASE-p1 heterodimer was removed by substituting Asn 14 with Leu. The Asn 14-->Leu variants are significantly more stable than the p1 peptides and preferentially form a heterotetramer instead of a 
heterodimer. Strikingly, the heterotetramer does not fold into a unique structure; in particular, the helices lack a unique orientation. Thus, the Asn 14 residue imparts specificity for formation of a two-stranded, parallel coiled coil at the expense of stability. The results suggest that, whereas nonspecific hydrophobic interactions contribute to protein stability, the requirement to satisfy the hydrogen bonding potential of buried polar residues in the generally hydrophobic environment of the protein interior can impart specificity (structural uniqueness) to protein folding and design.},
  Institution              = {Howard Hughes Medical Institute, Department of Biology, Cambridge, Massachusetts 02142, USA.},
  Keywords                 = {Amino Acid Sequence; Anilino Naphthalenesulfonates, chemistry; Asparagine, chemistry; Circular Dichroism; Fluorescent Dyes, chemistry; Hydrogen Bonding; Hydrogen, chemistry; Hydrogen-Ion Concentration; Molecular Sequence Data; Protein Conformation; Protein Folding; Protein Structure, Secondary; Proteins, chemistry; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {7612604},
  Timestamp                = {2010.09.22}
}

@Article{Lynch2012,
  Title                    = {Evolutionary layering and the limits to cellular perfection},
  Author                   = {Lynch, Michael},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2012},
  Number                   = {46},
  Pages                    = {18851--18856},
  Volume                   = {109},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2015.06.24}
}

@Article{Lynch2007,
  Title                    = {The frailty of adaptive hypotheses for the origins of organismal complexity.},
  Author                   = {Michael Lynch},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2007},

  Month                    = {May},
  Pages                    = {8597--8604},
  Volume                   = {104 Suppl 1},

  Abstract                 = {The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory. Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive forces of genetic drift and mutation. In addition, emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization. These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes, with the population-genetic environment imposing strong 
directionality on the paths that are open to evolutionary exploitation.},
  Institution              = {Department of Biology, Indiana University, Bloomington, IN 47405, USA. milynch@indiana.edu},
  Keywords                 = {Adaptation, Biological; Alleles; Animals; Biological Evolution; Genome, genetics; Humans; Models, Biological; Mutation, genetics},
  Owner                    = {ranjan},
  Pii                      = {0702207104},
  Pmid                     = {17494740},
  Timestamp                = {2010.12.14}
}

@Article{Lynch2006,
  Title                    = {The origins of eukaryotic gene structure.},
  Author                   = {Lynch, Michael},
  Journal                  = {Mol Biol Evol},
  Year                     = {2006},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {450--468},
  Volume                   = {23},

  Abstract                 = {Most of the phenotypic diversity that we perceive in the natural world is directly attributable to the peculiar structure of the eukaryotic gene, which harbors numerous embellishments relative to the situation in prokaryotes. The most profound changes include introns that must be spliced out of precursor mRNAs, transcribed but untranslated leader and trailer sequences (untranslated regions), modular regulatory elements that drive patterns of gene expression, and expansive intergenic regions that harbor additional diffuse control mechanisms. Explaining the origins of these features is difficult because they each impose an intrinsic disadvantage by increasing the genic mutation rate to defective alleles. To address these issues, a general hypothesis for the emergence of eukaryotic gene structure is provided here. Extensive information on absolute population sizes, recombination rates, and mutation rates strongly supports the view that eukaryotes have reduced genetic effective 
population sizes relative to prokaryotes, with especially extreme reductions being the rule in multicellular lineages. The resultant increase in the power of random genetic drift appears to be sufficient to overwhelm the weak mutational disadvantages associated with most novel aspects of the eukaryotic gene, supporting the idea that most such changes are simple outcomes of semi-neutral processes rather than direct products of natural selection. However, by establishing an essentially permanent change in the population-genetic environment permissive to the genome-wide repatterning of gene structure, the eukaryotic condition also promoted a reliable resource from which natural selection could secondarily build novel forms of organismal complexity. Under this hypothesis, arguments based on molecular, cellular, and/or physiological constraints are insufficient to explain the disparities in gene, genomic, and phenotypic complexity between prokaryotes and eukaryotes.},
  Institution              = {Department of Biology, Indiana University, Bloomington, USA. milynch@indiana.edu},
  Keywords                 = {Animals; Eukaryotic Cells; Evolution, Molecular; Genome, genetics; Humans; Mutation; RNA Splicing, genetics; RNA, Messenger, genetics; Recombination, Genetic; Selection, Genetic},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {msj050},
  Pmid                     = {16280547},
  Timestamp                = {2012.09.21}
}

@Article{Lynch2006a,
  Title                    = {Streamlining and simplification of microbial genome architecture},
  Author                   = {Lynch, Michael},
  Journal                  = {Annu. Rev. Microbiol.},
  Year                     = {2006},
  Pages                    = {327--349},
  Volume                   = {60},

  Owner                    = {ranjan},
  Publisher                = {Annual Reviews},
  Timestamp                = {2015.06.24}
}

@Article{Lynch2003,
  Title                    = {The origins of genome complexity.},
  Author                   = {Lynch, Michael and Conery, John S.},
  Journal                  = {Science},
  Year                     = {2003},

  Month                    = {Nov},
  Number                   = {5649},
  Pages                    = {1401--1404},
  Volume                   = {302},

  Abstract                 = {Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size. According to this model, much of the restructuring of eukaryotic genomes was initiated by nonadaptive processes, and this in turn provided novel substrates for the secondary evolution of phenotypic complexity by natural selection. The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies.},
  Institution              = {Department of Biology, Indiana University, Bloomington, IN 47405, USA. mlynch@bio.indiana.edu},
  Keywords                 = {Alleles; Animals; Bacteria, genetics; Body Constitution; Eukaryota, genetics; Evolution, Molecular; Fungi, genetics; Gene Duplication; Gene Silencing; Genetic Drift; Genetic Variation; Genome; Humans; Interspersed Repetitive Sequences; Introns; Invertebrates, genetics; Mutation; Phylogeny; Plants, genetics; Population Density; Recombination, Genetic; Selection, Genetic; Spliceosomes; Vertebrates, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {302/5649/1401},
  Pmid                     = {14631042},
  Timestamp                = {2012.09.21}
}

@Book{Lynch2007a,
  Title                    = {The origins of genome architecture},
  Author                   = {Lynch, Michael and Walsh, Bruce},
  Publisher                = {Sinauer Associates Sunderland},
  Year                     = {2007},
  Volume                   = {98},

  Owner                    = {ranjan},
  Timestamp                = {2015.06.24}
}

@Article{Feig2004,
  Title                    = {MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.},
  Author                   = {Feig M. and Karanicolas J. and Brooks C.L.~3rd},
  Journal                  = {J Mol Graph Model.},
  Year                     = {2004},
  Number                   = {5},
  Pages                    = {377--395},
  Volume                   = {22},

  Owner                    = {ranjan},
  Timestamp                = {2016.08.28}
}

@Article{Muller1929,
  Title                    = {The Connection between the Zig-Zag Structure of the Hydrocarbon Chain and the Alternations in the Properties of Odd and Even Numbered Chain Compounds},
  Author                   = {ALEX M\"{U}LLER},
  Journal                  = {Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character},
  Year                     = {1929},
  Number                   = {794},
  Pages                    = {317--321},
  Volume                   = {124},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Maayan2009,
  Title                    = {Folded biomimetic oligomers for enantioselective catalysis.},
  Author                   = {Maayan, Galia and Ward, Michael D. and Kirshenbaum, Kent},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2009},

  Month                    = {Aug},
  Number                   = {33},
  Pages                    = {13679--13684},
  Volume                   = {106},

  Abstract                 = {Many naturally occurring biopolymers (i.e., proteins, RNA, DNA) owe their unique properties to their well-defined three-dimensional structures. These attributes have inspired the design and synthesis of folded architectures with functions ranging from molecular recognition to asymmetric catalysis. Among these are synthetic oligomeric peptide ("foldamer") mimics, which can display conformational ordering at short chain lengths. Foldamers, however, have not been explored as platforms for asymmetric catalysis. This report describes a library of synthetic helical "peptoid" oligomers that enable enantioselective transformations at an embedded achiral catalytic center, as illustrated by the oxidative kinetic resolution of 1-phenylethanol. In an investigation aimed at elucidating key structure-function relationships, we have discovered that the enantioselectivity of the catalytic peptoids depends on the handedness of the asymmetric environment derived from the helical scaffold, the 
position of the catalytic center along the peptoid backbone, and the degree of conformational ordering of the peptoid scaffold. The transfer of chiral information from a folded scaffold can enable the use of a diverse assortment of embedded achiral catalytic centers, promising a generation of synthetic foldamer catalysts for enantioselective transformations that can be performed under a broad range of reaction environments.},
  Institution              = {Department of Chemistry and Molecular Design Institute, New York University, 100 Washington Square East, New York, NY 10003-6688, USA.},
  Keywords                 = {Benzyl Alcohols, chemistry; Biomimetics; Catalysis; Chromatography, Gas, methods; Circular Dichroism; Cyclic N-Oxides, chemistry; Kinetics; Models, Chemical; Models, Molecular; Molecular Conformation; Oxygen, chemistry; Peptides, chemistry; Protein Structure, Tertiary; Stereoisomerism; Temperature},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {0903187106},
  Pmid                     = {19667204},
  Timestamp                = {2012.07.15}
}

@Book{MacGillivray2010,
  Title                    = {Metal-organic frameworks: design and application},
  Author                   = {MacGillivray, Leonard R},
  Publisher                = {John Wiley \& Sons},
  Year                     = {2010},

  Owner                    = {ranjan},
  Timestamp                = {2015.03.22}
}

@Article{charmm_ff98,
  Title                    = {{All-Atom Empirical Potential for Molecular Modeling and Dynamics studies of Proteins}},
  Author                   = {Alexander D. {MacKerell Jr.} and D. Bashford and M. Bellott and R. L. {Dunbrack Jr.} and J. D. Evanseck and M. J. Field and S. Fischer and J. Gao and H. Guo and S. Ha and D. Joseph-McCarthy and L. Kuchnir and K. Kuczera and F. T. K. Lau and C. Mattos and S. Michnick and T. Ngo and D. T. Nguyen and B. Prodhom and W. E. Reiher, III and B. Roux and M. Schlenkrich and J. C. Smith and R. Stote and J. Straub and M. Watanabe and J. Wi{\'o}rkiewicz-Kuczera and D. Yin and M. Karplus},
  Journal                  = {J. Phys. Chem. B},
  Year                     = {1998},
  Pages                    = {307},
  Volume                   = {102}
}

@Article{MacKerell2000,
  Title                    = {Development and current status of the CHARMM force field for nucleic acids.},
  Author                   = {MacKerell, Jr, AD and Banavali, N. and Foloppe, N.},
  Journal                  = {Biopolymers},
  Year                     = {2000},
  Number                   = {4},
  Pages                    = {257--265},
  Volume                   = {56},

  Abstract                 = {The CHARMM27 all-atom force field for nucleic acids represents a highly optimized model for investigations of nucleic acids via empirical force field calculations. The force field satisfactorily treats the A, B, and Z forms of DNA as well as RNA, and it also useful for nucleosides and nucleotides. In addition, it is compatible with the CHARMM force fields for proteins and lipids, allowing for simulation studies of heterogeneous systems.},
  Institution              = {Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 N. Pine Street, Baltimore, MD 21201, USA. alex@outerbanks.umaryland.edu},
  Keywords                 = {Biophysics, methods/trends; Computer Simulation; Nucleic Acids, chemistry; Reproducibility of Results; Static Electricity; Structure-Activity Relationship},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {3.0.CO;2-W},
  Pmid                     = {11754339},
  Timestamp                = {2012.06.21}
}

@Article{Madras1993,
  Title                    = {The self-avoiding random walk},
  Author                   = {Madras, Neal and Slade, Gordon},
  Journal                  = {Probability and its applications. Birkh},
  Year                     = {1993},

  Owner                    = {ranjan},
  Timestamp                = {2013.07.06}
}

@Article{Maeso2012,
  Title                    = {Widespread recurrent evolution of genomic features},
  Author                   = {Maeso, Ignacio and Roy, Scott William and Irimia, Manuel},
  Journal                  = {Genome biology and evolution},
  Year                     = {2012},
  Number                   = {4},
  Pages                    = {486--500},
  Volume                   = {4},

  Owner                    = {ranjan},
  Publisher                = {Oxford University Press},
  Timestamp                = {2015.06.24}
}

@Article{Manna2009,
  Title                    = {Evolutionary constraints on hub and non-hub proteins in human protein interaction network: insight from protein connectivity and intrinsic disorder},
  Author                   = {Manna, Baisali and Bhattacharya, Tanusree and Kahali, Bratati and Ghosh, Tapash Chandra},
  Journal                  = {Gene},
  Year                     = {2009},
  Number                   = {1},
  Pages                    = {50--55},
  Volume                   = {434},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.12.06}
}

@Article{Mannige2008,
  Title                    = {Tilable nature of virus capsids and the role of topological constraints in natural capsid design.},
  Author                   = {Mannige, R.V. and {Brooks III}, C.L.},
  Journal                  = PRE,
  Year                     = {2008},
  Number                   = {5},
  Pages                    = {051902},
  Volume                   = {77},

  File                     = {Mannige2008.pdf:pdfs/Mannige2008.pdf:PDF}
}

@Article{Mannige2015a,
  Title                    = {Landscape of kinetically trapped binary assemblies},
  Author                   = {Mannige, Ranjan V},
  Journal                  = {The Journal of chemical physics},
  Year                     = {2015},
  Number                   = {21},
  Pages                    = {214902},
  Volume                   = {143},

  Owner                    = {ranjan},
  Publisher                = {AIP Publishing},
  Timestamp                = {2016.03.28}
}

@Article{Mannige2013b,
  Title                    = {Origination of the Protein Fold Repertoire from Oily Pluripotent Peptides},
  Author                   = {Ranjan V Mannige},
  Journal                  = {Proteomes},
  Year                     = {2014},
  Number                   = {2},
  Pages                    = {154-168},
  Volume                   = {2},

  Owner                    = {ranjan},
  Timestamp                = {2013.12.05}
}

@Article{Mannige2014b,
  Title                    = {Dynamic New World: Refining Our View of Protein Structure, Function and Evolution},
  Author                   = {Ranjan V Mannige},
  Journal                  = {Proteomes},
  Year                     = {2014},
  Number                   = {1},
  Pages                    = {128-153},
  Volume                   = {2},

  Owner                    = {ranjan},
  Timestamp                = {2014.06.10}
}

@Article{Mannige2013a,
  Title                    = {Two regimes of protein evolution and their unique dependencies on sequence composition},
  Author                   = {Ranjan V. Mannige},
  Journal                  = PRE,
  Year                     = {2013},
  Number                   = {6},
  Pages                    = {062714},
  Volume                   = {87},

  Owner                    = {ranjan},
  Timestamp                = {2011.12.03}
}

@Book{Mannige2010c,
  Title                    = {Principles of Virus Capsid Design.},
  Author                   = {Ranjan V. Mannige},
  Publisher                = {ProQuest (Dissertation)},
  Year                     = {2010},
  Number                   = {9781109683769},

  Owner                    = {ranjan},
  Timestamp                = {2010.12.13}
}

@Article{Mannige2012,
  Title                    = {A universal trend among proteomes indicates an oily last common ancestor.},
  Author                   = {Mannige, Ranjan V. and {Brooks III}, Charles L. and Shakhnovich, Eugene I.},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2012},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {e1002839},
  Volume                   = {8}
}

@Article{Mannige2010,
  Title                    = {Periodic table of virus capsids: implications for natural selection and design.},
  Author                   = {Ranjan V Mannige and Charles L Brooks},
  Journal                  = {PLoS One},
  Year                     = {2010},
  Number                   = {3},
  Pages                    = {e9423},
  Volume                   = {5},

  Abstract                 = {BACKGROUND: For survival, most natural viruses depend upon the existence of spherical capsids: protective shells of various sizes composed of protein subunits. So far, general evolutionary pressures shaping capsid design have remained elusive, even though an understanding of such properties may help in rationally impeding the virus life cycle and designing efficient nano-assemblies. PRINCIPAL FINDINGS: This report uncovers an unprecedented and species-independent evolutionary pressure on virus capsids, based on the the notion that the simplest capsid designs (or those capsids with the lowest "hexamer complexity", C(h)) are the fittest, which was shown to be true for all available virus capsids. The theories result in a physically meaningful periodic table of virus capsids that uncovers strong and overarching evolutionary pressures, while also offering geometric explanations to other capsid properties (rigidity, pleomorphy, auxiliary requirements, etc.) that were previously 
considered to be unrelatable properties of the individual virus. SIGNIFICANCE: Apart from describing a universal rule for virus capsid evolution, our work (especially the periodic table) provides a language with which highly diverse virus capsids, unified only by geometry, may be described and related to each other. Finally, the available virus structure databases and other published data reiterate the predicted geometry-derived rules, reinforcing the role of geometry in the natural selection and design of virus capsids.},
  Institution              = {Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan, United States of America. ranjan@umich.edu},
  Owner                    = {ranjan},
  Pmid                     = {20209096},
  Timestamp                = {2010.06.08}
}

@Article{Mannige2009,
  Title                    = {Geometric considerations in virus capsid size specificity, auxiliary requirements, and buckling.},
  Author                   = {Ranjan V Mannige and Charles L Brooks},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2009},

  Month                    = {May},
  Number                   = {21},
  Pages                    = {8531--8536},
  Volume                   = {106},

  Abstract                 = {Spherical capsids are shells of protein subunits that protect the genomes of many viral strains. Although nature displays a range of spherical capsid sizes (reflected by the number of subunits in the formation), specific strains display stringent requirements for forming capsids of specific sizes, a requirement that appears crucial to infectivity. Despite its importance in pathogenicity, little is known regarding the determinants of capsid size. Still less is known about exactly which capsids can undergo maturation events such as buckling transitions--postcapsid-assembly events that are crucial to some virus strains. We show that the exclusive determinant of capsid size is hexamer shape, as defined by subunit-subunit dihedral angles. This conclusion arises from considering the dihedral angle patterns within hexamers belonging to natural canonical capsids and geometric capsid models (deltahedra). From simple geometric models and an understanding of endo angle propagation 
discussed here, we then suggest that buckling transitions may be available only to capsids of certain size (specifically, T < 7 capsids are precluded from such transformations) and that T > 7 capsids require the help of auxiliary mechanisms for proper capsid formation. These predictions, arising from simple geometry and modeling, are backed by a body of empirical evidence, further reinforcing the extent to which the evolution of the atomistically complex virus capsid may be principled around simple geometric design/requirements.},
  Institution              = {Department of Molecular Biology and Center for Theoretical Biological Physics, The Scripps Research Institute, 10550 North Torrey Pines Court, TPC 6, La Jolla, CA 92037, USA. ranjan@umich.edu},
  Keywords                 = {Capsid, chemistry; Crystallography, X-Ray; Substrate Specificity; Viral Proteins, chemistry},
  Owner                    = {ranjan},
  Pii                      = {0811517106},
  Pmid                     = {19439655},
  Timestamp                = {2010.06.08}
}

@Article{Mannige2015,
  Title                    = {Peptoid nanosheets exhibit a new secondary structure motif},
  Author                   = {R. V. Mannige and T. K. Haxton and C. Proulx and E. J. Robertson and A. Battigelli and G. L. Butterfoss and R. N. Zuckermann and S Whitelam},
  Journal                  = {Nature},
  Year                     = {2015},
  Pages                    = {415--420},
  Volume                   = {526},

  Owner                    = {ranjan},
  Timestamp                = {2014.11.17}
}

@Article{Mannige2016,
  author       = {R. V. Mannige and J. Kundu and S. Whitelam},
  title        = {The {R}amachandran number: an order parameter for protein geometry},
  journal      = {PLoS One},
  journaltitle = {PLoS One},
  year         = {2016},
  volume       = {11},
  number       = {8},
  pages        = {e0160023},
  owner        = {ranjan},
  timestamp    = {2014.11.17},
}

@Article{Mannige2015b,
  Title                    = {Predicting the outcome of the growth of binary solids far from equilibrium},
  Author                   = {R. V. Mannige and S. Whitelam},
  Journal                  = PRE,
  Year                     = {2016},
  Pages                    = {042136},
  Volume                   = {93},

  Owner                    = {ranjan},
  Timestamp                = {2015.06.01}
}

@Article{Marahiel1997,
  Title                    = {Modular Peptide Synthetases Involved in Nonribosomal Peptide Synthesis.},
  Author                   = {Mohamed A. Marahiel and Torsten Stachelhaus and Henning D. Mootz},
  Journal                  = {Chem Rev},
  Year                     = {1997},

  Month                    = {Nov},
  Number                   = {7},
  Pages                    = {2651--2674},
  Volume                   = {97},

  Institution              = {Biochemie/Fachbereich Chemie, Hans-Meerwein-Strasse, Philipps-Universit?t Marburg, 35032 Marburg, Germany.},
  Owner                    = {ranjan},
  Pii                      = {cr960029e},
  Pmid                     = {11851476},
  Timestamp                = {2010.02.08}
}

@Article{Marashi2004,
  Title                    = {Correlations between genomic GC levels and optimal growth temperatures are not 'robust'.},
  Author                   = {Marashi, Sayed-Amir and Ghalanbor, Zahra},
  Journal                  = {Biochem Biophys Res Commun},
  Year                     = {2004},

  Month                    = {Dec},
  Number                   = {2},
  Pages                    = {381--383},
  Volume                   = {325},

  Abstract                 = {Musto et al. [FEBS Lett. 573 (2004) 73] studied the correlations between GC levels and optimal growth temperatures in 20 prokaryotic families. They reported that positive correlations are generally observed, and many of these are significant. Here, we have shown that these correlations are not "robust," i.e., correlation coefficients and/or significance of correlations can be considerably influenced by exclusion of very few (even as small as one) species from each dataset. The sensitivity of correlations is assumed as a result of high levels of bias in the family datasets. We concluded that solely based on these data, one cannot establish that GC contents of prokaryotic genomes increase as a result of growth temperature increments.},
  Institution              = {Department of Biotechnology, Faculty of Science, University of Tehran, Enghelab Ave., Tehran, Iran. marashie@khayan.ut.ac.ir},
  Keywords                 = {Adaptation, Physiological; Bacteria, genetics/growth /&/ development; Base Composition, physiology; Genome, Bacterial; Prokaryotic Cells, physiology; Statistics as Topic; Temperature},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0006-291X(04)02369-1},
  Pmid                     = {15530402},
  Timestamp                = {2012.09.26}
}

@Article{Marchalonis2001,
  Title                    = {Exquisite specificity and peptide epitope recognition promiscuity, properties shared by antibodies from sharks to humans.},
  Author                   = {J. J. Marchalonis and M. K. Adelman and I. F. Robey and S. F. Schluter and A. B. Edmundson},
  Journal                  = {J Mol Recognit},
  Year                     = {2001},
  Number                   = {2},
  Pages                    = {110--121},
  Volume                   = {14},

  Abstract                 = {This review considers definitions of the specificity of antibodies including the development of recent concepts of recognition polyspecificity and epitope promiscuity. Using sets of homologous and unrelated peptides derived from the sequences of immunoglobulin and T cell receptor chains we offer operational definitions of cross-reactivity by investigating correlations of either identities in amino acid sequence, or in hydrophobicity/hydrophilicity profiles with degree of binding in enzyme-linked immunosorbent assays. Polyreactivity, or polyspecificity, are terms used to denote binding of a monoclonal antibody or purified antibody preparation to large complex molecules that are structurally unrelated, such as thyroglobulin and DNA. As a first approximation, there is a linear correlation between degree of sequence identity or hydrophobicity/hydrophilicity and antigenic cross-binding. However, catastrophic interchanges of amino acids can occur where changing of one amino acid out 
of 16 in a synthetic peptide essentially eliminates binding to certain antibodies. An operational definition of epitope promiscuity for peptides is the case where two peptides show little or no identity in amino acid sequence but bind strongly to the same antibody as shown by either direct binding or competitive inhibition. Analysis of antibodies of humans and sharks, the two most divergent species in evolution to express antibodies and the combinatorial immune response, indicates that the capacity for both exquisite specificity and epitope recognition promiscuity are essential conserved features of individual vertebrate antibodies.},
  Institution              = {Microbiology and Immunology, College of Medicine, University of Arizona, Tucson, Arizona, USA. diannah@u.arizona.edu},
  Keywords                 = {Amino Acid Sequence; Animals; Antibodies, Monoclonal, immunology; Antibody Specificity; Antigens, chemistry/immunology; Autoantibodies; Binding Sites, Antibody; Enzyme-Linked Immunosorbent Assay; Epitopes, B-Lymphocyte, immunology; Humans; Immunoglobulin Heavy Chains; Immunoglobulin Light Chains; Molecular Sequence Data; Peptides, chemistry/immunology; Receptors, Antigen, T-Cell; Sharks, immunology; Species Specificity},
  Owner                    = {ranjan},
  Pii                      = {10.1002/jmr.527},
  Pmid                     = {11301481},
  Timestamp                = {2010.09.22}
}

@Article{Marelja1974,
  Title                    = {Chain ordering in liquid crystals. I. Evenodd effect},
  Author                   = {S. Marelja},
  Journal                  = {J. Chem. Phys.},
  Year                     = {1974},
  Pages                    = {3599--3604},
  Volume                   = {60},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Marigoliash1963,
  Title                    = {Primary structure and evolution of cytochrome C.},
  Author                   = {E. Marigoliash},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1963},

  Month                    = {Oct},
  Pages                    = {672--679},
  Volume                   = {50},

  Keywords                 = {Amino Acids; Cytochromes; Evolution; Fishes; Horses; Physiology, Comparative; Poultry; Rabbits; Research; Swine; Yeasts},
  Owner                    = {ranjan},
  Pmid                     = {14077496},
  Timestamp                = {2010.02.07}
}

@Article{Markegard2015,
  Title                    = {Coarse-Grained Simulation Study of Sequence Effects on DNA Hybridization in a Concentrated Environment},
  Author                   = {Markegard, Cade B and Fu, Iris W and Reddy, K Anki and Nguyen, Hung D},
  Journal                  = {The Journal of Physical Chemistry B},
  Year                     = {2015},
  Number                   = {5},
  Pages                    = {1823--1834},
  Volume                   = {119},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2015.09.16}
}

@Article{Martins1997,
  Title                    = {Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data},
  Author                   = {Emilia P. Martins and Thomas F Hansen},
  Journal                  = {The American Naturalist},
  Year                     = {1997},
  Number                   = {4},
  Pages                    = {646--667},
  Volume                   = {149},

  Owner                    = {ranjan},
  Timestamp                = {2012.03.11}
}

@InCollection{Mascarenhas2009,
  Title                    = {Fidelity mechanisms of the aminoacyl-tRNA synthetases},
  Author                   = {Mascarenhas, AP and An, S and Rosen, AE and Martinis, SA and Musier-Forsyth, K},
  Booktitle                = {Protein Engineering},
  Publisher                = {Springer},
  Year                     = {2009},
  Pages                    = {155--203},

  Owner                    = {ranjan},
  Timestamp                = {2013.11.17}
}

@Article{Maslov2007,
  Title                    = {Propagation of large concentration changes in reversible protein-binding networks.},
  Author                   = {Sergei Maslov and I. Ispolatov},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2007},

  Month                    = {Aug},
  Number                   = {34},
  Pages                    = {13655--13660},
  Volume                   = {104},

  Abstract                 = {We study how the dynamic equilibrium of the reversible protein-protein-binding network in yeast Saccharomyces cerevisiae responds to large changes in abundances of individual proteins. The magnitude of shifts between free and bound concentrations of their immediate and more distant neighbors in the network is influenced by such factors as the network topology, the distribution of protein concentrations among its nodes, and the average binding strength. Our primary conclusion is that, on average, the effects of a perturbation are strongly localized and exponentially decay with the network distance away from the perturbed node, which explains why, despite globally connected topology, individual functional modules in such networks are able to operate fairly independently. We also found that under specific favorable conditions, realized in a significant number of paths in the yeast network, concentration perturbations can selectively propagate over considerable network distances (up 
to four steps). Such "action-at-a-distance" requires high concentrations of heterodimers along the path as well as low free (unbound) concentration of intermediate proteins.},
  Institution              = {Department of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, NY 11973, USA. maslov@bnl.gov},
  Keywords                 = {Computer Simulation; Protein Binding; Proteins, metabolism; Saccharomyces cerevisiae, metabolism},
  Owner                    = {ranjan},
  Pii                      = {0702905104},
  Pmid                     = {17699619},
  Timestamp                = {2011.07.05}
}

@Article{Matsuurua2014,
  Title                    = {Rational design of self-assembled proteins and peptides for nano-and micro-sized architectures},
  Author                   = {Matsuurua, Kazunori},
  Journal                  = {RSC Advances},
  Year                     = {2014},
  Number                   = {6},
  Pages                    = {2942--2953},
  Volume                   = {4},

  Owner                    = {ranjan},
  Publisher                = {Royal Society of Chemistry},
  Timestamp                = {2014.08.29}
}

@Article{Matthews1967,
  Title                    = {Peptide synthesis from hydrogen cyanide and water.},
  Author                   = {C. N. Matthews and R. E. Moser},
  Journal                  = {Nature},
  Year                     = {1967},

  Month                    = {Sep},
  Number                   = {5107},
  Pages                    = {1230--1234},
  Volume                   = {215},

  Keywords                 = {Amino Acids, analysis; Ammonia; Biogenesis; Chromatography, Gel; Cyanides; Methane; Peptides, analysis/chemical synthesis; Water},
  Owner                    = {ranjan},
  Pmid                     = {6052719},
  Timestamp                = {2009.12.06}
}

@Article{Maulucci2008,
  Title                    = {Synthesis, structures, and properties of nine-, twelve-, and eighteen-membered N-benzyloxyethyl cyclic $\alpha$-peptoids},
  Author                   = {Maulucci, N and Izzo, I and Bifulco, G and Aliberti, A and De Cola, C and Comegna, D and Gaeta, C and Napolitano, A and Pizza, C and Tedesco, C and others},
  Journal                  = {Chemical Communications},
  Year                     = {2008},
  Number                   = {33},
  Pages                    = {3927--3929},

  Owner                    = {ranjan},
  Publisher                = {Royal Society of Chemistry},
  Timestamp                = {2015.04.16}
}

@Article{Mayor1962,
  Title                    = {Icosahedral Models and Viruses: A Critical Evaluation.},
  Author                   = {Mayor,H.D. and Melnick,J.L.},
  Journal                  = {Science.},
  Year                     = {1962},
  Pages                    = {613-615},
  Volume                   = {137},

  File                     = {Mayor1962.pdf:pdfs/Mayor1962.pdf:PDF}
}

@Article{McDonald2006,
  Title                    = {Apparent trends of amino Acid gain and loss in protein evolution due to nearly neutral variation.},
  Author                   = {John H McDonald},
  Journal                  = {Mol Biol Evol},
  Year                     = {2006},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {240--244},
  Volume                   = {23},

  Abstract                 = {It has recently been claimed that certain amino acids have been increasing in frequency in all living organisms for most of the history of life on earth, while other amino acids have been decreasing in frequency. Three lines of evidence have been offered for this assertion, but each has a more plausible alternative interpretation. Here I show that unequal patterns of gains and losses for particular pairs of amino acids (such as more leucine --> phenylalanine than phenylalanine --> leucine substitutions in humans and chimpanzees since they split from a common ancestor) are consistent with a simple neutral model at equilibrium amino acid frequencies. Unequal numbers of gains and losses for particular amino acids (such as more gains than losses of cysteine) are shown by simulations to be consistent with a model of nearly neutral evolution. Unequal numbers of gains and losses for particular amino acids in human polymorphism data are shown by simulations to be explainable by the 
nearly neutral model as well. In a comparison of protein sequences from four strains of Escherichia coli, polarized by one outgroup strain of Salmonella, the disparity in number of gains and losses for particular amino acids is strong in terminal branches but weaker or nonexistent in internal branches, which is inconsistent with the universal trend model but as expected under the nearly neutral model.},
  Institution              = {Department of Biological Sciences, University of Delaware, USA. mcdonald@udel.edu},
  Keywords                 = {Amino Acid Substitution; Amino Acids, genetics; Escherichia coli Proteins, genetics; Escherichia coli, genetics; Evolution, Molecular; Humans; Models, Genetic; Salmonella, genetics},
  Owner                    = {ranjan},
  Pii                      = {msj026},
  Pmid                     = {16195487},
  Timestamp                = {2010.06.26}
}

@Book{McNaught1997,
  Title                    = {Compendium of chemical terminology},
  Author                   = {McNaught, Alan D and Wilkinson, Andrew},
  Publisher                = {Blackwell Science Oxford},
  Year                     = {1997},
  Volume                   = {1669},

  Owner                    = {ranjan},
  Timestamp                = {2013.11.10}
}

@Article{Mendez2010,
  Title                    = {Mutation bias favors protein folding stability in the evolution of small populations.},
  Author                   = {Mendez, Raul and Fritsche, Miriam and Porto, Markus and Bastolla, Ugo},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2010},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {e1000767},
  Volume                   = {6},

  Abstract                 = {Mutation bias in prokaryotes varies from extreme adenine and thymine (AT) in obligatory endosymbiotic or parasitic bacteria to extreme guanine and cytosine (GC), for instance in actinobacteria. GC mutation bias deeply influences the folding stability of proteins, making proteins on the average less hydrophobic and therefore less stable with respect to unfolding but also less susceptible to misfolding and aggregation. We study a model where proteins evolve subject to selection for folding stability under given mutation bias, population size, and neutrality. We find a non-neutral regime where, for any given population size, there is an optimal mutation bias that maximizes fitness. Interestingly, this optimal GC usage is small for small populations, large for intermediate populations and around 50\% for large populations. This result is robust with respect to the definition of the fitness function and to the protein structures studied. Our model suggests that small populations 
evolving with small GC usage eventually accumulate a significant selective advantage over populations evolving without this bias. This provides a possible explanation to the observation that most species adopting obligatory intracellular lifestyles with a consequent reduction of effective population size shifted their mutation spectrum towards AT. The model also predicts that large GC usage is optimal for intermediate population size. To test these predictions we estimated the effective population sizes of bacterial species using the optimal codon usage coefficients computed by dos Reis et al. and the synonymous to non-synonymous substitution ratio computed by Daubin and Moran. We found that the population sizes estimated in these ways are significantly smaller for species with small and large GC usage compared to species with no bias, which supports our prediction.},
  Keywords                 = {Bacteria, genetics; Bacterial Proteins, chemistry/genetics/metabolism; Base Composition; Computer Simulation; Evolution, Molecular; Genetic Fitness; Models, Genetic; Mutation; Protein Folding; Protein Stability; Proteins, chemistry/genetics; Species Specificity},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pmid                     = {20463869},
  Timestamp                = {2012.07.09}
}

@Article{Mettenleiter2009,
  Title                    = {Herpesvirus assembly: an update.},
  Author                   = {Thomas C Mettenleiter and Barbara G Klupp and Harald Granzow},
  Journal                  = {Virus Res},
  Year                     = {2009},

  Month                    = {Aug},
  Number                   = {2},
  Pages                    = {222--234},
  Volume                   = {143},

  Abstract                 = {The order Herpesvirales contains viruses infecting animals from molluscs to men with a common virion morphology which have been classified into the families Herpesviridae, Alloherpesviridae and Malacoherpesviridae. Herpes virions are among the most complex virus particles containing a multitude of viral and cellular proteins which assemble into nucleocapsid, envelope and tegument. After autocatalytic assembly of the capsid and packaging of the newly replicated viral genome, a process which occurs in the nucleus and resembles head formation and genome packaging in the tailed double-stranded DNA bacteriophages, the nucleocapsid is translocated to the cytoplasm by budding at the inner nuclear membrane followed by fusion of the primary envelope with the outer nuclear membrane. Viral and cellular proteins are involved in mediating this 'nuclear egress' which entails substantial remodeling of the nuclear architecture. For final maturation within the cytoplasm tegument components 
associate with the translocated nucleocapsid, with themselves, and with the future envelope containing viral membrane proteins in a complex network of interactions resulting in the formation of an infectious herpes virion. The diverse interactions between the involved proteins exhibit a striking redundancy which is still insufficiently understood. In this review, recent advances in our understanding of the molecular processes resulting in herpes virion maturation will be presented and discussed as an update of a previous contribution [Mettenleiter, T.C., 2004. Budding events in herpesvirus morphogenesis. Virus Res. 106, 167-180].},
  Institution              = {Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany. thomas.mettenleiter@fli.bund.de},
  Keywords                 = {Animals; DNA, Viral, metabolism; Herpesviridae, physiology; Humans; Viral Proteins, metabolism; Virus Assembly},
  Owner                    = {ranjan},
  Pii                      = {S0168-1702(09)00118-X},
  Pmid                     = {19651457},
  Timestamp                = {2009.12.25}
}

@Article{Meyerguz2004,
  Title                    = {Computational analysis of sequence selection mechanisms.},
  Author                   = {Leonid Meyerguz and Catherine Grasso and Jon Kleinberg and Ron Elber},
  Journal                  = {Structure},
  Year                     = {2004},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {547--557},
  Volume                   = {12},

  Abstract                 = {Mechanisms leading to gene variations are responsible for the diversity of species and are important components of the theory of evolution. One constraint on gene evolution is that of protein foldability; the three-dimensional shapes of proteins must be thermodynamically stable. We explore the impact of this constraint and calculate properties of foldable sequences using 3660 structures from the Protein Data Bank. We seek a selection function that receives sequences as input, and outputs survival probability based on sequence fitness to structure. We compute the number of sequences that match a particular protein structure with energy lower than the native sequence, the density of the number of sequences, the entropy, and the "selection" temperature. The mechanism of structure selection for sequences longer than 200 amino acids is approximately universal. For shorter sequences, it is not. We speculate on concrete evolutionary mechanisms that show this behavior.},
  Institution              = {Department of Computer Science, 4130 Upson Hall, Cornell University, Ithaca, NY 14853, USA.},
  Keywords                 = {Computer Simulation; Databases, Protein; Evolution, Molecular; Models, Molecular; Protein Folding; Selection, Genetic; Temperature; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0969212604000607},
  Pmid                     = {15062078},
  Timestamp                = {2011.10.30}
}

@Article{Midic2009,
  Title                    = {Protein disorder in the human diseasome: unfoldomics of human genetic diseases.},
  Author                   = {Midic, Uros and Oldfield, Christopher J. and Dunker, A Keith and Obradovic, Zoran and Uversky, Vladimir N.},
  Journal                  = {BMC Genomics},
  Year                     = {2009},
  Pages                    = {S12},
  Volume                   = {10 Suppl 1},

  Abstract                 = {Intrinsically disordered proteins lack stable structure under physiological conditions, yet carry out many crucial biological functions, especially functions associated with regulation, recognition, signaling and control. Recently, human genetic diseases and related genes were organized into a bipartite graph (Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690). This diseasome network revealed several significant features such as the common genetic origin of many diseases.We analyzed the abundance of intrinsic disorder in these diseasome network proteins by means of several prediction algorithms, and we analyzed the functional repertoires of these proteins based on prior studies relating disorder to function. Our analyses revealed that (i) Intrinsic disorder is common in proteins associated with many human genetic diseases; (ii) Different disease classes vary in the IDP contents of their associated 
proteins; (iii) Molecular recognition features, which are relatively short loosely structured protein regions within mostly disordered sequences and which gain structure upon binding to partners, are common in the diseasome, and their abundance correlates with the intrinsic disorder level; (iv) Some disease classes have a significant fraction of genes affected by alternative splicing, and the alternatively spliced regions in the corresponding proteins are predicted to be highly disordered; and (v) Correlations were found among the various diseasome graph-related properties and intrinsic disorder.These observations provide the basis for the construction of the human-genetic-disease-associated unfoldome.},
  Doi                      = {10.1186/1471-2164-10-S1-S12},
  Institution              = {Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA. uros@ist.temple.edu},
  Keywords                 = {Algorithms; Alternative Splicing; Computational Biology; Databases, Protein; Humans; Protein Conformation; Protein Folding; Proteins, metabolism; Proteomics; Structure-Activity Relationship},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {1471-2164-10-S1-S12},
  Pmid                     = {19594871},
  Timestamp                = {2013.12.08}
}

@Article{Miklos2011,
  Title                    = {Protein crowding tunes protein stability.},
  Author                   = {Andrew C Miklos and Mohona Sarkar and Yaqiang Wang and Gary J Pielak},
  Journal                  = {J Am Chem Soc},
  Year                     = {2011},

  Month                    = {May},
  Number                   = {18},
  Pages                    = {7116--7120},
  Volume                   = {133},

  Abstract                 = {Thirty percent of a cell's volume is filled with macromolecules, and protein chemistry in a crowded environment is predicted to differ from that in dilute solution. We quantified the effect of crowding by globular proteins on the equilibrium thermodynamic stability of a small globular protein. Theory has long predicted that crowding should stabilize proteins, and experiments using synthetic polymers as crowders show such stabilizing effects. We find that protein crowders can be mildly destabilizing. The destabilization arises from a competition between stabilizing excluded-volume effects and destabilizing nonspecific interactions, including electrostatic interactions. This competition results in tunable stability, which could impact our understanding of the spatial and temporal roles of proteins in living systems.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Miklos2011.pdf:PDF},
  Institution              = {Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.},
  Keywords                 = {Muramidase, chemistry; Povidone, chemistry; Protein Conformation; Protein Folding; Protein Stability; Serum Albumin, Bovine, chemistry; Solutions; Static Electricity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {21506571},
  Timestamp                = {2011.11.27}
}

@Article{Miller1953,
  Title                    = {A production of amino acids under possible primitive earth conditions.},
  Author                   = {S. L. Miller},
  Journal                  = {Science},
  Year                     = {1953},

  Month                    = {May},
  Number                   = {3046},
  Pages                    = {528--529},
  Volume                   = {117},

  File                     = {Miller1953.pdf:pdfs/Miller1953.pdf:PDF},
  Keywords                 = {Amino Acids},
  Owner                    = {ranjan},
  Pmid                     = {13056598},
  Timestamp                = {2009.09.21}
}

@Article{Miller1997,
  Title                    = {Oparin's ``Origin of Life'': sixty years later.},
  Author                   = {Miller, S. L. and Schopf, J. W. and Lazcano, A.},
  Journal                  = {J Mol Evol},
  Year                     = {1997},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {351--353},
  Volume                   = {44},

  Institution              = {U CA, Los Angeles},
  Keywords                 = {Biogenesis; Books, history; History, 20th Century; Russia},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9089073},
  Timestamp                = {2012.04.06}
}

@Article{Mindell1990,
  Title                    = {Mode of allozyme evolution: Increased genetic distance associated with speciation events},
  Author                   = {Mindell,D.P. and Sites,J.W. and Graur,D.},
  Journal                  = {J. evol. Biol},
  Year                     = {1990},
  Pages                    = {125--131},
  Volume                   = {3},

  File                     = {:/home/ranjan/research/jabref/pdfs/Mindell1990.pdf:PDF},
  Owner                    = {ranjan},
  Timestamp                = {2011.04.26}
}

@Article{Mindell1990b,
  Title                    = {Assessing The Relationship Between Speciation And Evolutionary Change.},
  Author                   = {David P. Mindell and Jack W. Sites Jr. and Dan Graur},
  Journal                  = {Cladistics},
  Year                     = {1990},
  Pages                    = {393--398},
  Volume                   = {6},

  Owner                    = {ranjan},
  Timestamp                = {2011.04.26}
}

@Article{Mirijanian2014,
  Title                    = {Development and use of an atomistic CHARMM-based forcefield for peptoid simulation.},
  Author                   = {Mirijanian, Dina T. and Mannige, Ranjan V. and Zuckermann, Ronald N. and Whitelam, Stephen},
  Journal                  = {J Comput Chem},
  Year                     = {2014},

  Month                    = {Feb},
  Number                   = {5},
  Pages                    = {360--370},
  Volume                   = {35}
}

@Article{Mirkin2003,
  Title                    = {Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.},
  Author                   = {Boris G Mirkin and Trevor I Fenner and Michael Y Galperin and Eugene V Koonin},
  Journal                  = {BMC Evol Biol},
  Year                     = {2003},

  Month                    = {Jan},
  Pages                    = {2},
  Volume                   = {3},

  Abstract                 = {BACKGROUND: Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. RESULTS: We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs). We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes) of almost 90\% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene 
loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains). We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain) are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA) of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties indicates that, even with a gain 
penalty of 1 (equal weights assigned to a gain and a loss), the set of 572 genes assigned to LUCA might be nearly sufficient to sustain a functioning organism. Under this gain penalty value, the numbers of horizontal gene transfer and gene loss events are nearly identical. This result holds true for two alternative topologies of the species tree and even under random shuffling of the tree. Therefore, the results seem to be compatible with approximately equal likelihoods of HGT and gene loss in the evolution of prokaryotes. CONCLUSIONS: The notion that gene loss and HGT are major aspects of prokaryotic evolution was supported by quantitative analysis of the mapping of the phyletic patterns of COGs onto a hypothetical species tree. Algorithms were developed for constructing parsimonious evolutionary scenarios, which include gene loss and gain events, for orthologous gene sets, given a species tree. This analysis shows, contrary to expectations, that the number of predicted HGT events that occurred during the 
evolution of prokaryotes might be approximately the same as the number of gene losses. The approach to the reconstruction of evolutionary scenarios employed here is conservative with regard to the detection of HGT because only patterns of gene presence-absence in sequenced genomes are taken into account. In reality, horizontal transfer might have contributed to the evolution of many other genes also, which makes it a dominant force in prokaryotic evolution.},
  Institution              = {School of Information Systems and Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK. mirkin@dcs.bbk.ac.uk},
  Keywords                 = {Algorithms; Amino Acid Sequence, genetics; Archaeal Proteins, chemistry/genetics; Bacterial Proteins, chemistry/genetics; Computational Biology, methods; Evolution, Molecular; Gene Deletion; Gene Transfer, Horizontal, genetics; Genome; Genome, Archaeal; Genome, Bacterial; Genome, Fungal; Mathematical Computing; Models, Genetic; Molecular Sequence Data; Saccharomyces cerevisiae Proteins, genetics},
  Owner                    = {ranjan},
  Pmid                     = {12515582},
  Timestamp                = {2010.06.26}
}

@Article{Mirny1998,
  Title                    = {How evolution makes proteins fold quickly.},
  Author                   = {L. A. Mirny and V. I. Abkevich and E. I. Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1998},

  Month                    = {Apr},
  Number                   = {9},
  Pages                    = {4976--4981},
  Volume                   = {95},

  Abstract                 = {Sequences of fast-folding model proteins (48 residues long on a cubic lattice) were generated by an evolution-like selection toward fast folding. We find that fast-folding proteins exhibit a specific folding mechanism in which all transition state conformations share a smaller subset of common contacts (folding nucleus). Acceleration of folding was accompanied by dramatic strengthening of interactions in the folding nucleus whereas average energy of nonnucleus interactions remained largely unchanged. Furthermore, the residues involved in the nucleus are the most conserved ones within families of evolved sequences. Our results imply that for each protein structure there is a small number of conserved positions that are key determinants of fast folding into that structure. This conjecture was tested on two protein superfamilies: the first having the classical monophosphate binding fold (CMBF; 98 families) and the second having type-III repeat fold (47 families). For each 
superfamily, we discovered a few positions that exhibit very strong and statistically significant "conservatism of conservatism"-amino acids in those positions are conserved within every family whereas the actual types of amino acids varied from family to family. Those amino acids are in spatial contact with each other. The experimental data of Serrano and coworkers [Lopez-Hernandez, E. & Serrano, L. (1996) Fold. Des. (London) 1, 43-55]. for one of the proteins of the CMBF superfamily (CheY) show that residues identified this way indeed belong to the folding nucleus. Further analysis revealed deep connections between nucleation in CMBF proteins and their function.},
  Institution              = {Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge MA 02138, USA.},
  Keywords                 = {Bacterial Proteins; Binding Sites; Computer Simulation; Evolution; Kinetics; Membrane Proteins, ultrastructure; Models, Molecular; Phosphates, metabolism; Point Mutation; Protein Conformation; Protein Folding; Structure-Activity Relationship},
  Owner                    = {ranjan},
  Pmid                     = {9560213},
  Timestamp                = {2009.12.05}
}

@Article{Mirny1999,
  Title                    = {Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function.},
  Author                   = {L. A. Mirny and E. I. Shakhnovich},
  Journal                  = {J Mol Biol},
  Year                     = {1999},

  Month                    = {Aug},
  Number                   = {1},
  Pages                    = {177--196},
  Volume                   = {291},

  Abstract                 = {Here, we provide an analysis of molecular evolution of five of the most populated protein folds: immunoglobulin fold, oligonucleotide-binding fold, Rossman fold, alpha/beta plait, and TIM barrels. In order to distinguish between "historic", functional and structural reasons for amino acid conservations, we consider proteins that acquire the same fold and have no evident sequence homology. For each fold we identify positions that are conserved within each individual family and coincide when non-homologous proteins are structurally superimposed. As a baseline for statistical assessment we use the conservatism expected based on the solvent accessibility. The analysis is based on a new concept of "conservatism-of-conservatism". This approach allows us to identify the structural features that are stabilized in all proteins having a given fold, despite the fact that actual interactions that provide such stabilization may vary from protein to protein. Comparison with experimental data 
on thermodynamics, folding kinetics and function of the proteins reveals that such universally conserved clusters correspond to either: (i) super-sites (common location of active site in proteins having common tertiary structures but not function) or (ii) folding nuclei whose stability is an important determinant of folding rate, or both (in the case of Rossman fold). The analysis also helps to clarify the relation between folding and function that is apparent for some folds.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.},
  Keywords                 = {Amino Acid Sequence; Conserved Sequence; Evolution, Molecular; Immunoglobulins, chemistry; Kinetics; Models, Molecular; Models, Statistical; Molecular Sequence Data; Mutation; Protein Folding; Sequence Homology, Amino Acid; Solvents, chemistry},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(99)92911-X},
  Pmid                     = {10438614},
  Timestamp                = {2009.12.05}
}

@Article{Mirny2001,
  Title                    = {Evolutionary conservation of the folding nucleus.},
  Author                   = {L. Mirny and E. Shakhnovich},
  Journal                  = {J Mol Biol},
  Year                     = {2001},

  Month                    = {Apr},
  Number                   = {2},
  Pages                    = {123--129},
  Volume                   = {308},

  Abstract                 = {Here, we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein (AcP) folding nucleus residues are significantly more conserved than the rest of the protein. Two aspects of our study are especially important: (i) grouping of amino acid residues into classes according to their physical-chemical properties and (ii) proper normalization of amino acid probabilities that reflects the fact that evolutionary pressure to conserve some amino acid types may itself affect concentration of various amino acid types in protein families. Neglect of any of those two factors may make physical and biological "signals" from conservation profiles disappear.},
  File                     = {Mirny2001.pdf:pdfs/Mirny2001.pdf:PDF},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA},
  Keywords                 = {Conserved Sequence; Evolution, Molecular; Kinetics; Models, Molecular; Mutation, genetics; Protein Conformation; Protein Folding; Proteins, chemistry/classification/genetics/metabolism; Statistics as Topic},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(01)94602-9},
  Pmid                     = {11327757},
  Timestamp                = {2009.09.21}
}

@Article{Mirny2001a,
  Title                    = {Protein folding theory: from lattice to all-atom models.},
  Author                   = {L. Mirny and E. Shakhnovich},
  Journal                  = {Annu Rev Biophys Biomol Struct},
  Year                     = {2001},
  Pages                    = {361--396},
  Volume                   = {30},

  Abstract                 = {This review focuses on recent advances in understanding protein folding kinetics in the context of nucleation theory. We present basic concepts such as nucleation, folding nucleus, and transition state ensemble and then discuss recent advances and challenges in theoretical understanding of several key aspects of protein folding kinetics. We cover recent topology-based approaches as well as evolutionary studies and molecular dynamics approaches to determine protein folding nucleus and analyze other aspects of folding kinetics. Finally, we briefly discuss successful all-atom Monte-Carlo simulations of protein folding and conclude with a brief outlook for the future.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA. leonid@origami.harvard.edu},
  Keywords                 = {Cell Nucleus, metabolism; Evolution, Molecular; Kinetics; Models, Molecular; Monte Carlo Method; Protein Folding; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {30/1/361},
  Pmid                     = {11340064},
  Timestamp                = {2009.12.05}
}

@Article{Misawa2008,
  Title                    = {The universal trend of amino acid gain-loss is caused by CpG hypermutability.},
  Author                   = {Kazuharu Misawa and Naoyuki Kamatani and Reiko F Kikuno},
  Journal                  = {J Mol Evol},
  Year                     = {2008},

  Month                    = {Oct},
  Number                   = {4},
  Pages                    = {334--342},
  Volume                   = {67},

  Abstract                 = {Understanding the cause of the changes in the amino acid composition of proteins is essential for understanding the evolution of protein functions. Since the early 1970s, it has been known that the frequency of some amino acids in protein sequences is increasing and that of others is decreasing. Recently, it was found that the trends of amino acid changes were similar in 15 taxa representing Bacteria, Archaea, and Eukaryota. However, the cause of this similarity in the trend of the gains and losses of amino acids continued to be debated. Here, we show that this trend of the gain and loss of amino acids can be simply explained by CpG hypermutability. We found that the frequency of amino acids coded by codons with TpG dinucleotides and those with CpA dinucleotides is increasing, while that of amino acids coded by codons with CpG dinucleotides is decreasing. We also found that organisms that lack DNA methyltransferase show different trends of the gain and loss of amino acids. DNA 
methyltransferase methylates CpG dinucleotides and induces CpG hypermutability. The incorporation of CpG hypermutability into models of protein evolution will improve studies on protein evolution in different organisms.},
  Institution              = {Chiba Industry Advancement Center, Chiba, Japan. kazumisawa@riken.jp},
  Keywords                 = {Amino Acids, genetics; Animals; Codon, genetics; CpG Islands, genetics; DNA (Cytosine-5-)-Methyltransferase, genetics; Humans; Models, Genetic; Mutagenesis, genetics; Mutation, genetics},
  Owner                    = {ranjan},
  Pmid                     = {18810523},
  Timestamp                = {2010.06.26}
}

@InCollection{Mitalipov2009,
  Title                    = {Totipotency, pluripotency and nuclear reprogramming},
  Author                   = {Mitalipov, Shoukhrat and Wolf, Don},
  Booktitle                = {Engineering of Stem Cells},
  Publisher                = {Springer},
  Year                     = {2009},
  Pages                    = {185--199},

  Owner                    = {ranjan},
  Timestamp                = {2013.07.01}
}

@Article{Mittal2014,
  Title                    = {Hamiltonian Switch Metropolis Monte Carlo simulations for improved conformational sampling of intrinsically disordered regions tethered to ordered domains of proteins},
  Author                   = {Mittal, Anuradha and Lyle, Nicholas and Harmon, Tyler S and Pappu, Rohit V},
  Journal                  = {Journal of chemical theory and computation},
  Year                     = {2014},
  Number                   = {8},
  Pages                    = {3550--3562},
  Volume                   = {10},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2015.09.17}
}

@Article{Miyazawa1996,
  Title                    = {Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.},
  Author                   = {S. Miyazawa and R. L. Jernigan},
  Journal                  = {J Mol Biol},
  Year                     = {1996},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {623--644},
  Volume                   = {256},

  Abstract                 = {Attractive inter-residue contact energies for proteins have been re-evaluated with the same assumptions and approximations used originally by us in 1985, but with a significantly larger set of protein crystal structures. An additional repulsive packing energy term, operative at higher densities to prevent overpacking, has also been estimated for all 20 amino acids as a function of the number of contacting residues, based on their observed distributions. The two terms of opposite sign are intended to be used together to provide an estimate of the overall energies of inter-residue interactions in simplified proteins without atomic details. To overcome the problem of how to utilize the many homologous proteins in the Protein Data Bank, a new scheme has been devised to assign different weights to each protein, based on similarities among amino acid sequences. A total of 1168 protein structures containing 1661 subunit sequences are actually used here. After the sequence weights have 
been applied, these correspond to an effective number of residue-residue contacts of 113,914, or about six times more than were used in the old analysis. Remarkably, the new attractive contact energies are nearly identical to the old ones, except for those with Leu and the rarer amino acids Trp and Met. The largest change found for Leu is surprising. The estimates of hydrophobicity from the contact energies for non-polar side-chains agree well with the experimental values. In an application of these contact energies, the sequences of 88 structurally distinct proteins in the Protein Data Bank are threaded at all possible positions without gaps into 189 different folds of proteins whose sequences differ from each other by at least 35\% sequence identity. The native structures for 73 of 88 proteins, excluding 15 exceptional proteins such as membrane proteins, are all demonstrated to have the lowest alignment energies.},
  Institution              = {Faculty of Technology Gunma Univrsity, Kiryu Gunma, Japan.},
  Keywords                 = {Amino Acids, chemistry; Computer Simulation; Databases, Factual; Mathematics; Protein Folding; Proteins, chemistry; Sequence Homology, Amino Acid},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(96)90114-X},
  Pmid                     = {8604144},
  Timestamp                = {2010.07.26}
}

@Article{Molton1978,
  Title                    = {Polymers to Living Cells: Molecules against Entropy},
  Author                   = {Molton,P.M.},
  Journal                  = {Journal of the British Interplanetary Society},
  Year                     = {1978},
  Pages                    = {147},
  Volume                   = {31},

  Owner                    = {ranjan},
  Timestamp                = {2010.05.12}
}

@Article{Moody1999,
  Title                    = {Geometry of phage head construction},
  Author                   = {Moody, M. F.},
  Journal                  = JMB,
  Year                     = {1999},
  Number                   = {2},
  Pages                    = {401--433},
  Volume                   = {293},

  File                     = {Moody1999.pdf:pdfs/Moody1999.pdf:PDF}
}

@Book{Morange1998,
  Title                    = {History of Molecular Biology, trans. by Matthew Cobb},
  Author                   = {Morange, Michel},
  Publisher                = {Harvard University Press, Cambridge, Mass.},
  Year                     = {1998},

  Owner                    = {ranjan},
  Timestamp                = {2013.12.03}
}

@Article{Moreno-Hagelsieb2008,
  Title                    = {Choosing BLAST options for better detection of orthologs as reciprocal best hits.},
  Author                   = {Gabriel Moreno-Hagelsieb and Kristen Latimer},
  Journal                  = {Bioinformatics},
  Year                     = {2008},

  Month                    = {Feb},
  Number                   = {3},
  Pages                    = {319--324},
  Volume                   = {24},

  Abstract                 = {The analyses of the increasing number of genome sequences requires shortcuts for the detection of orthologs, such as Reciprocal Best Hits (RBH), where orthologs are assumed if two genes each in a different genome find each other as the best hit in the other genome. Two BLAST options seem to affect alignment scores the most, and thus the choice of a best hit: the filtering of low information sequence segments and the algorithm used to produce the final alignment. Thus, we decided to test whether such options would help better detect orthologs.Using Escherichia coli K12 as an example, we compared the number and quality of orthologs detected as RBH. We tested four different conditions derived from two options: filtering of low-information segments, hard (default) versus soft; and alignment algorithm, default (based on matching words) versus Smith-Waterman. All options resulted in significant differences in the number of orthologs detected, with the highest numbers obtained with the 
combination of soft filtering with Smith-Waterman alignments. We compared these results with those of Reciprocal Shortest Distances (RSD), supposed to be superior to RBH because it uses an evolutionary measure of distance, rather than BLAST statistics, to rank homologs and thus detect orthologs. RSD barely increased the number of orthologs detected over those found with RBH. Error estimates, based on analyses of conservation of gene order, found small differences in the quality of orthologs detected using RBH. However, RSD showed the highest error rates. Thus, RSD have no advantages over RBH.Orthologs detected as Reciprocal Best Hits using soft masking and Smith-Waterman alignments can be downloaded from http://popolvuh.wlu.ca/Orthologs.},
  Institution              = {Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada, N2L 3C5. gmoreno@wlu.ca},
  Keywords                 = {Base Sequence; Chromosome Mapping, methods; DNA, Bacterial, genetics; Database Management Systems; Databases, Genetic; Escherichia coli, genetics; Molecular Sequence Data; Proteins, genetics; Sequence Alignment, methods; Sequence Analysis, DNA, methods; Sequence Homology, Nucleic Acid},
  Owner                    = {ranjan},
  Pii                      = {btm585},
  Pmid                     = {18042555},
  Timestamp                = {2011.04.18}
}

@Article{Morgan2006,
  Title                    = {Why there was a useful plausible analogy between geodesic domes and spherical viruses},
  Author                   = {Morgan, G.J.},
  Journal                  = {Hist Philos Life Sci.},
  Year                     = {2006},
  Number                   = {2},
  Pages                    = {215--235},
  Volume                   = {28}
}

@Article{Morgan2003,
  Title                    = {Historical review: viruses, crystals and geodesic domes},
  Author                   = {Morgan, G.J.},
  Journal                  = {Trends Biochem Sci.},
  Year                     = {2003},
  Number                   = {2},
  Pages                    = {86--90},
  Volume                   = {28},

  File                     = {:pdfs/Morgan2003.pdf:PDF}
}

@Article{Morrison2006,
  Title                    = {A lock-and-key model for protein--protein interactions},
  Author                   = {Morrison, Julie L and Breitling, Rainer and Higham, Desmond J and Gilbert, David R},
  Journal                  = {Bioinformatics},
  Year                     = {2006},
  Number                   = {16},
  Pages                    = {2012--2019},
  Volume                   = {22},

  Owner                    = {ranjan},
  Publisher                = {Oxford Univ Press},
  Timestamp                = {2013.11.17}
}

@Article{Mossel2005,
  Title                    = {Random biochemical networks: the probability of self-sustaining autocatalysis.},
  Author                   = {Mossel, Elchanan and Steel, Mike},
  Journal                  = {J Theor Biol},
  Year                     = {2005},

  Month                    = {Apr},
  Number                   = {3},
  Pages                    = {327--336},
  Volume                   = {233},

  Abstract                 = {We determine conditions under which a random biochemical system is likely to contain a subsystem that is both autocatalytic and able to survive on some ambient 'food' source. Such systems have previously been investigated for their relevance to origin-of-life models. In this paper we extend earlier work, by finding precisely the order of catalysation required for the emergence of such self-sustaining autocatalytic networks. This answers questions raised in earlier papers, yet also allows for a more general class of models. We also show that a recently described polynomial-time algorithm for determining whether a catalytic reaction system contains an autocatalytic, self-sustaining subsystem is unlikely to adapt to allow inhibitory catalysation--in this case we show that the associated decision problem is NP-complete.},
  Institution              = {Statistics Department, UC Berkeley, CA, USA. mossel@stat.berkeley.edu},
  Keywords                 = {Biochemical Phenomena; Catalysis; Homeostasis; Models, Chemical; Probability},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0022-5193(04)00482-5},
  Pmid                     = {15652142},
  Timestamp                = {2012.04.05}
}

@Article{Moult2011,
  Title                    = {Critical assessment of methods of protein structure prediction (CASP)--round IX},
  Author                   = {Moult, John and Fidelis, Krzysztof and Kryshtafovych, Andriy and Tramontano, Anna},
  Journal                  = {Proteins: Structure, Function, and Bioinformatics},
  Year                     = {2011},
  Number                   = {S10},
  Pages                    = {1--5},
  Volume                   = {79},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2013.11.19}
}

@Article{Moure2011,
  Title                    = {Chemical modulation of peptoids: synthesis and conformational studies on partially constrained derivatives.},
  Author                   = {Moure, Alejandra and Sanclimens, Gl{\`o}ria and Bujons, Jordi and Masip, Isabel and Alvarez-Larena, Angel and P{\'e}rez-Pay{\'a}, Enrique and Alfonso, Ignacio and Messeguer, Angel},
  Journal                  = {Chemistry},
  Year                     = {2011},

  Month                    = {Jul},
  Number                   = {28},
  Pages                    = {7927--7939},
  Volume                   = {17},

  Abstract                 = {The high conformational flexibility of peptoids can generate problems in biomolecular selectivity as a result of undesired off-target interactions. This drawback can be counterbalanced by restricting the original flexibility to a certain extent, thus leading to new peptidomimetics. By starting from the structure of an active peptoid as an apoptosis inhibitor, we designed two families of peptidomimetics that bear either 7-substituted perhydro-1,4-diazepine-2,5-dione 2 or 3-substituted 1,4-piperazine-2,5-dione 3 moieties. We report an efficient, solid-phase-based synthesis for both peptidomimetic families 2 and 3 from a common intermediate. An NMR spectroscopic study of 2a,b and 3a,b showed two species in solution in different solvents that interconvert slowly on the NMR timescale. The cis/trans isomerization around the exocyclic tertiary amide bond is responsible for this conformational behavior. The cis isomers are more favored in nonpolar environments, and this preference is 
higher for the six-membered-ring derivative 3a,b. We propose that the hydrogen-bonding pattern could play an important role in the cis/trans equilibrium process. These hydrogen bonds were characterized in solution, in the solid state (i.e., by using X-ray studies), and by molecular modeling of simplified systems. A comparative study of a model peptoid 10 containing the isolated tertiary amide bond under study outlined the importance of the heterocyclic moiety for the prevalence of the cis configuration in 2a and 3a. The kinetics of the cis/trans interconversion in 2a, 3a, and 10 was also studied by variable-temperature NMR spectroscopic analysis. The full line-shape analysis of the NMR spectra of 10 revealed negligible entropic contribution to the energetic barrier in this conformational process. A theoretical analysis of 10 supported the results observed by NMR spectroscopic analysis. Overall, these results are relevant for the study of the peptidomimetic/biological-target interactions.},
  Institution              = {Department of Chemical and Biomolecular Nanotechnology, Instituto de Qu{\'i}mica Avanzada de Catalu{\~n}a, Consejo Superior de Investigaciones Cient{\'i}ficas, J. Girona, 18, 08034 Barcelona, Spain.},
  Keywords                 = {Amides, chemistry; Crystallography, X-Ray; Drug Design; Hydrogen Bonding; Isomerism; Magnetic Resonance Spectroscopy; Molecular Structure; Peptidomimetics, chemical synthesis/chemistry; Peptoids, chemical synthesis/chemistry; Protein Conformation},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {21611988},
  Timestamp                = {2012.06.19}
}

@Article{Mudd1932,
  Title                    = {A hypothetical mechanism of antibody formation},
  Author                   = {Mudd, Stuart},
  Journal                  = {The Journal of Immunology},
  Year                     = {1932},
  Number                   = {6},
  Pages                    = {423--427},
  Volume                   = {23},

  Owner                    = {ranjan},
  Publisher                = {Am Assoc Immnol},
  Timestamp                = {2013.12.03}
}

@Article{Murnen2013,
  Title                    = {Persistence length of polyelectrolytes with precisely located charges},
  Author                   = {Murnen, Hannah K and Rosales, Adrianne M and Dobrynin, Andrey V and Zuckermann, Ronald N and Segalman, Rachel A},
  Journal                  = {Soft Matter},
  Year                     = {2013},
  Number                   = {1},
  Pages                    = {90--98},
  Volume                   = {9},

  Owner                    = {ranjan},
  Publisher                = {Royal Society of Chemistry},
  Timestamp                = {2014.06.11}
}

@Article{Murphy2000,
  Title                    = {Simplified amino acid alphabets for protein fold recognition and implications for folding.},
  Author                   = {L. R. Murphy and A. Wallqvist and R. M. Levy},
  Journal                  = {Protein Eng},
  Year                     = {2000},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {149--152},
  Volume                   = {13},

  Abstract                 = {Protein design experiments have shown that the use of specific subsets of amino acids can produce foldable proteins. This prompts the question of whether there is a minimal amino acid alphabet which could be used to fold all proteins. In this work we make an analogy between sequence patterns which produce foldable sequences and those which make it possible to detect structural homologs by aligning sequences, and use it to suggest the possible size of such a reduced alphabet. We estimate that reduced alphabets containing 10-12 letters can be used to design foldable sequences for a large number of protein families. This estimate is based on the observation that there is little loss of the information necessary to pick out structural homologs in a clustered protein sequence database when a suitable reduction of the amino acid alphabet from 20 to 10 letters is made, but that this information is rapidly degraded when further reductions in the alphabet are made.},
  File                     = {Murphy2000.pdf:pdfs/Murphy2000.pdf:PDF},
  Institution              = {Department of Chemistry, Rutgers University, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, NJ 08854-8087, USA.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Amino Acids; Protein Folding; Proteins, chemistry; Sequence Alignment; Software},
  Owner                    = {ranjan},
  Pmid                     = {10775656},
  Timestamp                = {2009.10.03}
}

@Article{Murphy1998,
  Title                    = {Punctuated Equilibrium or Gradualism in the Lizard Genus Sceloporus? Lost in Plesiograms and a Forest of Trees},
  Author                   = {Robert W. Murphy and Nathan R. Lovejoy},
  Journal                  = {Cladistics},
  Year                     = {1998},
  Pages                    = {95--103},
  Volume                   = {14},

  Owner                    = {ranjan},
  Timestamp                = {2011.04.26}
}

@Article{Murray2008,
  Title                    = {Bovine viral diarrhea virus core is an intrinsically disordered protein that binds RNA},
  Author                   = {Murray, Catherine L and Marcotrigiano, Joseph and Rice, Charles M},
  Journal                  = {Journal of virology},
  Year                     = {2008},
  Number                   = {3},
  Pages                    = {1294--1304},
  Volume                   = {82},

  Owner                    = {ranjan},
  Publisher                = {Am Soc Microbiol},
  Timestamp                = {2013.11.17}
}

@Article{Murzin2008,
  Title                    = {Biochemistry. Metamorphic proteins.},
  Author                   = {Alexey G Murzin},
  Journal                  = {Science},
  Year                     = {2008},

  Month                    = {Jun},
  Number                   = {5884},
  Pages                    = {1725--1726},
  Volume                   = {320},

  File                     = {Murzin2008.pdf:pdfs/Murzin2008.pdf:PDF},
  Institution              = { CB2 0QH, UK. agm@mrc-lmb.cam.ac.uk},
  Keywords                 = {Bacterial Proteins, chemistry; Cell Cycle Proteins, chemistry/metabolism; DNA-Binding Proteins, chemistry; Dimerization; Evolution, Molecular; Hydrogen Bonding; Lymphokines, chemistry/genetics/metabolism; Models, Molecular; Point Mutation; Protein Conformation; Protein Folding; Repressor Proteins, chemistry; Sialoglycoproteins, chemistry/genetics/metabolism; Viral Regulatory and Accessory Proteins, chemistry},
  Owner                    = {ranjan},
  Pii                      = {320/5884/1725},
  Pmid                     = {18583598},
  Timestamp                = {2010.09.02}
}

@Article{Murzin1995,
  Title                    = {SCOP: a structural classification of proteins database for the investigation of sequences and structures.},
  Author                   = {A. G. Murzin and S. E. Brenner and T. Hubbard and C. Chothia},
  Journal                  = {J Mol Biol},
  Year                     = {1995},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {536--540},
  Volume                   = {247},

  Abstract                 = {To facilitate understanding of, and access to, the information available for protein structures, we have constructed the Structural Classification of Proteins (scop) database. This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure. It also provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references. Two search facilities are available. The homology search permits users to enter a sequence and obtain a list of any structures to which it has significant levels of sequence similarity. The key word search finds, for a word entered by the user, matches from both the text of the scop database and the headers of Brookhaven Protein Databank structure files. The database is freely accessible on World Wide Web (WWW) with an entry point to URL http: parallel scop.mrc-lmb.cam.ac.uk magnitude of scop.},
  Institution              = {MRC Laboratory of Molecular Biology and Centre for Protein Engineering, Cambridge, England.},
  Keywords                 = {Amino Acid Sequence; Databases, Factual; Protein Folding; Proteins, chemistry/classification; Sequence Analysis},
  Owner                    = {ranjan},
  Pii                      = {S0022283685701593},
  Pmid                     = {7723011},
  Timestamp                = {2010.12.27}
}

@Article{Musto2004,
  Title                    = {Correlations between genomic GC levels and optimal growth temperatures in prokaryotes.},
  Author                   = {Musto, H\'{e}ctor and Naya, Hugo and Zavala, Alejandro and Romero, H\'{e}ctor and Alvarez-Val\'{i}n, Fernando and Bernardi, Giorgio},
  Journal                  = {FEBS Lett},
  Year                     = {2004},

  Month                    = {Aug},
  Number                   = {1-3},
  Pages                    = {73--77},
  Volume                   = {573},

  Abstract                 = {In prokaryotes, GC levels range from 25\% to 75\%, and Topt from approximately 0 degrees C to >100 degrees C. When all species are considered together, no correlation is found between the two variables. Correlations are found, however, when Families of prokaryotes are analysed. Indeed, when Families comprising at least 10 species were studied (a set of 20 Families), positive correlations are found for 15 of them. Furthermore, a comparative analysis by independent contrasts made within the Families in order to control for phylogenetic non-independence showed qualitatively equivalent results. We conclude that Topt is one of the factors that influences genomic GC in prokaryotes.},
  Keywords                 = {Bacteria, genetics/growth /&/ development; Base Composition; DNA, Bacterial, genetics; Genome, Bacterial; Phylogeny; Prokaryotic Cells, cytology/metabolism; RNA, Ribosomal, genetics; Temperature},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0014579304009342},
  Pmid                     = {15327978},
  Timestamp                = {2012.09.26}
}

@Article{Nakagawa2003,
  Title                    = {The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins.},
  Author                   = {Nakagawa, A. and Miyazaki, N. and Taka, J. and Naitow, H. and Ogawa, A. and Fujimoto, Z. and Mizuno, H. and Higashi, T. and Watanabe, Y. and Omura, T. and Cheng, R. H. and Tsukihara, T.},
  Journal                  = {Structure.},
  Year                     = {2003},
  Number                   = {10},
  Pages                    = {1227--1238},
  Volume                   = {11},

  File                     = {Nakagawa2003.pdf:pdfs/Nakagawa2003.pdf:PDF}
}

@Article{Nakagawa2006,
  Title                    = {The inherent structure landscape of a protein},
  Author                   = {Nakagawa, Naoko and Peyrard, Michel},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2006},
  Number                   = {14},
  Pages                    = {5279--5284},
  Volume                   = {103},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2015.06.29}
}

@Article{Nam2010,
  Title                    = {Free-floating ultrathin two-dimensional crystals from sequence-specific peptoid polymers.},
  Author                   = {Nam, Ki Tae and Shelby, Sarah A. and Choi, Philip H. and Marciel, Amanda B. and Chen, Ritchie and Tan, Li and Chu, Tammy K. and Mesch, Ryan A. and Lee, Byoung-Chul and Connolly, Michael D. and Kisielowski, Christian and Zuckermann, Ronald N.},
  Journal                  = {Nat Mater},
  Year                     = {2010},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {454--460},
  Volume                   = {9},

  Abstract                 = {The design and synthesis of protein-like polymers is a fundamental challenge in materials science. A biomimetic approach is to explore the impact of monomer sequence on non-natural polymer structure and function. We present the aqueous self-assembly of two peptoid polymers into extremely thin two-dimensional (2D) crystalline sheets directed by periodic amphiphilicity, electrostatic recognition and aromatic interactions. Peptoids are sequence-specific, oligo-N-substituted glycine polymers designed to mimic the structure and functionality of proteins. Mixing a 1:1 ratio of two oppositely charged peptoid 36mers of a specific sequence in aqueous solution results in the formation of giant, free-floating sheets with only 2.7 nm thickness. Direct visualization of aligned individual peptoid chains in the sheet structure was achieved using aberration-corrected transmission electron microscopy. Specific binding of a protein to ligand-functionalized sheets was also demonstrated. The 
synthetic flexibility and biocompatibility of peptoids provide a flexible and robust platform for integrating functionality into defined 2D nanostructures.},
  Doi                      = {10.1038/nmat2742},
  Institution              = {Molecular Foundry; National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.},
  Keywords                 = {Amino Acid Sequence; Biomimetics; Buffers; Crystallization; Fourier Analysis; Glycine, analogs /&/ derivatives; Ligands; Models, Chemical; Nanostructures, chemistry/ultrastructure; Peptoids, chemistry; Polymers, chemical synthesis/chemistry; Protein Binding; Protein Structure, Secondary; Sequence Homology, Amino Acid; Static Electricity; Water, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nmat2742},
  Pmid                     = {20383129},
  Timestamp                = {2014.04.26}
}

@Article{Nandel2011,
  Title                    = {Peptoids with aliphatic sidechains as helical structures without hydrogen bonds and collagen/inverse-collagen type structures},
  Author                   = {Nandel, Fateh S and Saini, Avneet and others},
  Journal                  = {Journal of Biophysical Chemistry},
  Year                     = {2011},
  Number                   = {01},
  Pages                    = {37},
  Volume                   = {2},

  Owner                    = {ranjan},
  Publisher                = {Scientific Research Publishing},
  Timestamp                = {2014.07.23}
}

@Article{Nandhagopal2002,
  Title                    = {The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus.},
  Author                   = {Narayanasamy Nandhagopal and Alan A Simpson and James R Gurnon and Xiadong Yan and Timothy S Baker and Michael V Graves and James L Van Etten and Michael G Rossmann},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2002},

  Month                    = {Nov},
  Number                   = {23},
  Pages                    = {14758--14763},
  Volume                   = {99},

  Abstract                 = {Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-A resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel beta-barrel, "jelly-roll" domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities 
among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-A diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus.},
  Institution              = {Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.},
  Keywords                 = {Capsid, chemistry/ultrastructure; Cryoelectron Microscopy; DNA Viruses, chemistry; Evolution, Molecular; Glycosylation; Models, Molecular; Protein Conformation; Protein Subunits, chemistry},
  Owner                    = {ranjan},
  Pii                      = {232580699},
  Pmid                     = {12411581},
  Timestamp                = {2010.02.04}
}

@Article{Nash1998,
  Title                    = {Comparative genomics: tracking chromosome evolution in the family ursidae using reciprocal chromosome painting.},
  Author                   = {W. G. Nash and J. Wienberg and M. A. Ferguson-Smith and J. C. Menninger and S. J. O'Brien},
  Journal                  = {Cytogenet Cell Genet},
  Year                     = {1998},
  Number                   = {3-4},
  Pages                    = {182--192},
  Volume                   = {83},

  Abstract                 = {The Ursidae family includes eight species, the karyotype of which diverges somewhat, in both chromosome number and morphology, from that of other families in the order Carnivora. The combination of consensus molecular phylogeny and high-resolution trypsin G-banded karyotype analysis has suggested that ancestral chromosomal fissions and at least two fusion events are associated with the development of the different ursid species. Here, we revisit this hypothesis by hybridizing reciprocal chromosome painting probes derived from the giant panda (Ailuropoda melanoleuca), domestic cat (Felis catus), and man (Homo sapiens) to representative bear species karyotypes. Comparative analysis of the different chromosome segment homologies allowed reconstruction of the genomic composition of a putative ancestral bear karyotype based upon the recognition of 39 chromosome segments defined by painting as the smallest conserved evolutionary unit segments (pSCEUS) among these species. The 
different pSCEUS combinations occurring among modern bear species support and extend the postulated sequence of chromosomal rearrangements and provide a framework to propose patterns of genome reorganization among carnivores and other mammal radiations.},
  Institution              = {W Cytogenetic Services, Inc., Lovettsville, VA, USA.},
  Keywords                 = {Animals; Cats; Chromosome Painting; Chromosomes, genetics; DNA Probes; Evolution, Molecular; Genome; Humans; Karyotyping; Ursidae, classification/genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {15176},
  Pmid                     = {10072575},
  Timestamp                = {2011.09.15}
}

@Article{Natarajan2005,
  Title                    = {Exploring icosahedral virus structures with VIPER},
  Author                   = {Natarajan,P. and Lander,G.C. and Shepherd,C.M. and Reddy,V.S. and Brooks III,C.L. and Johnson,J.E.},
  Journal                  = {Nat Rev Microbiol.},
  Year                     = {2005},
  Number                   = {10},
  Pages                    = {809-817},
  Volume                   = {3},

  File                     = {Natarajan2005.pdf:pdfs/Natarajan2005.pdf:PDF}
}

@Book{Nelson2005,
  Title                    = {Lehninger's Principles of Biochemistry},
  Author                   = {Nelson DL, Cox MM},
  Publisher                = {New York, New York: W. H. Freeman and Company.},
  Year                     = {2005},
  Edition                  = {4},

  Owner                    = {ranjan},
  Timestamp                = {2013.03.01}
}

@Article{Neuman2005,
  Title                    = {Complementarity in the supramolecular design of arenaviruses and retroviruses revealed by electron cryomicroscopy and image analysis.},
  Author                   = {Neuman,B.W. and Adair,B.D. and Burns,J.W. and Milligan,R.A. and Buchmeier,M.J. and Yeager,M.},
  Journal                  = {J Virol.},
  Year                     = {2005},
  Number                   = {6},
  Pages                    = {3822--3830},
  Volume                   = {79},

  File                     = {Neuman2005.pdf:pdfs/Neuman2005.pdf:PDF}
}

@Article{Nguyen2009,
  Title                    = {Invariant polymorphism in virus capsid assembly},
  Author                   = {Nguyen, Hung D and Reddy, Vijay S and Brooks III, Charles L},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {2009},
  Number                   = {7},
  Pages                    = {2606--2614},
  Volume                   = {131},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2015.07.21}
}

@Article{Nguyen2007,
  Title                    = {Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids},
  Author                   = {Nguyen, H. D. and Reddy, V. S. and Brooks III, C. L.},
  Journal                  = NANO,
  Year                     = {2007},
  Number                   = {2},
  Pages                    = {338-344},
  Volume                   = {7},

  File                     = {Nguyen2007.pdf:pdfs/Nguyen2007.pdf:PDF}
}

@Article{Nguyen2005,
  Title                    = {Elasticity theory and shape transitions of viral shells},
  Author                   = {Nguyen,T.T. and Bruinsma,R.F. and Gelbart,W.M.},
  Journal                  = PRE,
  Year                     = {2005},
  Number                   = {5 Pt 1},
  Pages                    = {051923},
  Volume                   = {72},

  File                     = {Nguyen2005.pdf:pdfs/Nguyen2005.pdf:PDF}
}

@Article{Nguyen2005a,
  Title                    = {An all-atom model of the pore-like structure of hexameric VP40 from Ebola: structural insights into the monomer-hexamer transition.},
  Author                   = {Tam Luong Nguyen and Guy Schoehn and Winfried Weissenhorn and Ann R Hermone and James C Burnett and Rekha G Panchal and Connor McGrath and Dan W Zaharevitz and M. Javad Aman and Rick Gussio and Sina Bavari},
  Journal                  = {J Struct Biol},
  Year                     = {2005},

  Month                    = {Jul},
  Number                   = {1},
  Pages                    = {30--40},
  Volume                   = {151},

  Abstract                 = {The matrix protein VP40 is an indispensable component of viral assembly and budding by the Ebola virus. VP40 is a monomer in solution, but can fold into hexameric and octameric states, two oligomeric conformations that play central roles in the Ebola viral life cycle. While the X-ray structures of monomeric and octameric VP40 have been determined, the structure of hexameric VP40 has only been solved by three-dimensional electron microscopy (EM) to a resolution of approximately 30 A. In this paper, we present the refinement of the EM reconstruction of truncated hexameric VP40 to approximately 20 A and the construction of an all-atom model (residues 44-212) using the EM model at approximately 20 A and the X-ray structure of monomeric VP40 as templates. The hexamer model suggests that the monomer-hexamer transition involves a conformational change in the N-terminal domain that is not evident during octamerization and therefore, may provide the basis for elucidating the biological 
function of VP40.},
  Institution              = {Target Structure-Based Drug Discovery Group, Developmental Therapeutics Program, SAIC, National Cancer Institute, Frederick, MD 21702, USA.},
  Keywords                 = {Microscopy, Electron; Models, Molecular; Nucleoproteins, chemistry; Protein Conformation; Viral Core Proteins, chemistry; X-Ray Diffraction},
  Owner                    = {ranjan},
  Pii                      = {S1047-8477(05)00064-X},
  Pmid                     = {15908231},
  Timestamp                = {2009.12.25}
}

@Article{Nijamudheena2010,
  Title                    = {Odd–even oscillations in structural and optical properties of gold clusters},
  Author                   = {A. Nijamudheena and Ayan Datta},
  Journal                  = {Journal of Molecular Structure: THEOCHEM},
  Year                     = {2010},
  Pages                    = {93–96},
  Volume                   = {945},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Nilsson2011,
  Title                    = {Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins.},
  Author                   = {Nilsson, Johan and Grahn, Mats and Wright, Anthony P H.},
  Journal                  = {Genome Biol},
  Year                     = {2011},
  Number                   = {7},
  Pages                    = {R65},
  Volume                   = {12},

  Abstract                 = {Understanding the adaptive changes that alter the function of proteins during evolution is an important question for biology and medicine. The increasing number of completely sequenced genomes from closely related organisms, as well as individuals within species, facilitates systematic detection of recent selection events by means of comparative genomics.We have used genome-wide strain-specific single nucleotide polymorphism data from 64 strains of budding yeast (Saccharomyces cerevisiae or Saccharomyces paradoxus) to determine whether adaptive positive selection is correlated with protein regions showing propensity for different classes of structure conformation. Data from phylogenetic and population genetic analysis of 3,746 gene alignments consistently shows a significantly higher degree of positive Darwinian selection in intrinsically disordered regions of proteins compared to regions of alpha helix, beta sheet or tertiary structure. Evidence of positive selection is 
significantly enriched in classes of proteins whose functions and molecular mechanisms can be coupled to adaptive processes and these classes tend to have a higher average content of intrinsically unstructured protein regions.We suggest that intrinsically disordered protein regions may be important for the production and maintenance of genetic variation with adaptive potential and that they may thus be of central significance for the evolvability of the organism or cell in which they occur.},
  Doi                      = {10.1186/gb-2011-12-7-r65},
  Institution              = {School of Life Sciences, Södertörn University, SE-141 89 Huddinge, Sweden. anthony.wright@ki.se},
  Keywords                 = {Adaptation, Biological; Codon; Genome, Fungal; Open Reading Frames; Polymorphism, Single Nucleotide; Protein Structure, Secondary; Proteins, chemistry/genetics; Proteome, genetics/metabolism; Saccharomycetales, genetics; Selection, Genetic; Species Specificity},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {gb-2011-12-7-r65},
  Pmid                     = {21771306},
  Timestamp                = {2013.12.12}
}

@Article{Nimwegen2000,
  Title                    = {Metastable evolutionary dynamics: crossing fitness barriers or escaping via neutral paths?},
  Author                   = {E. van Nimwegen and J. P. Crutchfield},
  Journal                  = {Bull Math Biol},
  Year                     = {2000},

  Month                    = {Sep},
  Number                   = {5},
  Pages                    = {799--848},
  Volume                   = {62},

  Abstract                 = {We analytically study the dynamics of evolving populations that exhibit metastability on the level of phenotype or fitness. In constant selective environments, such metastable behavior is caused by two qualitatively different mechanisms. On the one hand, populations may become pinned at a local fitness optimum, being separated from higher-fitness genotypes by a fitness barrier of low-fitness genotypes. On the other hand, the population may only be metastable on the level of phenotype or fitness while, at the same time, diffusing over neutral networks of selectively neutral genotypes. Metastability occurs in this case because the population is separated from higher-fitness genotypes by an entropy barrier: the population must explore large portions of these neutral networks before it discovers a rare connection to fitter phenotypes. We derive analytical expressions for the barrier crossing times in both the fitness barrier and entropy barrier regime. In contrast with 'landscape' 
evolutionary models, we show that the waiting times to reach higher fitness depend strongly on the width of a fitness barrier and much less on its height. The analysis further shows that crossing entropy barriers is faster by orders of magnitude than fitness barrier crossing. Thus, when populations are trapped in a metastable phenotypic state, they are most likely to escape by crossing an entropy barrier, along a neutral path in genotype space. If no such escape route along a neutral path exists, a population is most likely to cross a fitness barrier where the barrier is narrowest, rather than where the barrier is shallowest.},
  Institution              = {Santa Fe Institute, NM 87501, USA. ?erik,chaos?@santafe.edu},
  Keywords                 = {Biological Evolution; Genetics, Population; Genotype; Models, Genetic; Models, Theoretical; Mutation; Phenotype; Selection, Genetic},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0092-8240(00)90180-0},
  Pmid                     = {11016086},
  Timestamp                = {2011.11.20}
}

@Article{Nishimura1986,
  Title                    = {Possible origin of n-alkanes with a remarkable even-to-odd predominance in recent marine sediments},
  Author                   = {Mitsugu NISHIMURA and Earl W. BAKER},
  Journal                  = {Geochimica et Cosmochimica Acta},
  Year                     = {1986},
  Pages                    = {299--305},
  Volume                   = {50},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Nobeli2009,
  Title                    = {Protein promiscuity and its implications for biotechnology.},
  Author                   = {Irene Nobeli and Angelo D Favia and Janet M Thornton},
  Journal                  = {Nat Biotechnol},
  Year                     = {2009},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {157--167},
  Volume                   = {27},

  Abstract                 = {Molecular recognition between proteins and their interacting partners underlies the biochemistry of living organisms. Specificity in this recognition is thought to be essential, whereas promiscuity is often associated with unwanted side effects, poor catalytic properties and errors in biological function. Recent experimental evidence suggests that promiscuity, not only in interactions but also in the actual function of proteins, is not as rare as was previously thought. This has implications not only for our fundamental understanding of molecular recognition and how protein function has evolved over time but also in the realm of biotechnology. Understanding protein promiscuity is becoming increasingly important not only to optimize protein engineering applications in areas as diverse as synthetic biology and metagenomics but also to lower attrition rates in drug discovery programs, identify drug interaction surfaces less susceptible to escape mutations and potentiate the power 
of polypharmacology.},
  File                     = {Nobeli2009.pdf:pdfs/Nobeli2009.pdf:PDF},
  Institution              = {Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK. i.nobeli@bbk.ac.uk},
  Keywords                 = {Animals; Biotechnology, trends; Computational Biology; Drug Design; Environment; Evolution, Molecular; Gene Expression Regulation; Humans; Ligands; Models, Molecular; Pliability; Protein Binding, physiology; Protein Conformation; Protein Engineering; Protein Folding; Protein Multimerization; Protein Processing, Post-Translational; Proteins, chemistry/physiology; Solvents; Structure-Activity Relationship},
  Owner                    = {ranjan},
  Pii                      = {nbt1519},
  Pmid                     = {19204698},
  Timestamp                = {2011.03.03}
}

@Article{Norman1997,
  Title                    = {Chemistry of the Elements},
  Author                   = {Norman, N and Greenwood, N and Earnshaw, A},
  Journal                  = {Butter worth-Heinemann, Earnshaw, Alan,},
  Year                     = {1997},

  Owner                    = {ranjan},
  Timestamp                = {2015.11.09}
}

@Article{Nourry2003,
  Title                    = {PDZ domain proteins: plug and play!},
  Author                   = {Claire Nourry and Seth G N Grant and Jean-Paul Borg},
  Journal                  = {Sci STKE},
  Year                     = {2003},

  Month                    = {Apr},
  Number                   = {179},
  Pages                    = {RE7},
  Volume                   = {2003},

  Abstract                 = {Protein-protein interactions are key elements in building functional protein complexes. Among the plethora of domains identified during the last 10 years, PDZ domains are one of the most commonly found protein-protein interaction domains in organisms from bacteria to humans. Although they may be the sole protein interaction domain within a cytoplasmic protein, they are most often found in combination with other protein interaction domains (for instance, SH3, PTB, WW) participating in complexes that facilitate signaling or determine the localization of receptors. Diversity of PDZ-containing protein function is provided by the large number of PDZ proteins that Mother Nature has distributed in the genome and implicates this protein family in the wiring of a huge number of molecules in molecular networks from the plasma membrane to the nucleus. Although at first sight their binding specificity appeared rather monotonous, involving only binding to the carboxyl-terminus of various 
proteins, it is now recognized that PDZ domains interact with greater versatility through PDZ-PDZ domain interaction; they bind to internal peptide sequences and even to lipids. Furthermore, PDZ domain-mediated interactions can sometimes be modulated in a dynamic way through target phosphorylation. In this review, we attempt to describe the structural basis of PDZ domain recognition and to give some functional insights into their role in the scaffolding of protein complexes implicated in normal and pathological biological processes.},
  Institution              = {U119 INSERM and Institut Paoli-Calmettes, Laboratory of Molecular Pharmacology, 27 Boulevard Le? Roure, 13009 Marseille, France.},
  Keywords                 = {Animals; Humans; Protein Binding, physiology; Protein Structure, Tertiary, physiology; Proteins, chemistry/classification/physiology; Repetitive Sequences, Amino Acid, physiology},
  Owner                    = {ranjan},
  Pii                      = {2003/179/re7},
  Pmid                     = {12709532},
  Timestamp                = {2009.06.21}
}

@Article{OBrien1990,
  Title                    = {Monotonicity of the number of self-avoiding walks},
  Author                   = {O'Brien, George L},
  Journal                  = {Journal of Statistical Physics},
  Year                     = {1990},
  Number                   = {3},
  Pages                    = {969--979},
  Volume                   = {59},

  Owner                    = {ranjan},
  Publisher                = {Springer},
  Timestamp                = {2013.07.06}
}

@Article{OBrien1999,
  Title                    = {Catalytic promiscuity and the evolution of new enzymatic activities},
  Author                   = {O'Brien, Patrick J and Herschlag, Daniel},
  Journal                  = {Chemistry \& biology},
  Year                     = {1999},
  Number                   = {4},
  Pages                    = {R91--R105},
  Volume                   = {6},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.30}
}

@Article{Oakley2011,
  Title                    = {Energy landscape and global optimization for a frustrated model protein.},
  Author                   = {Mark T Oakley and David J Wales and Roy L Johnston},
  Journal                  = {J Phys Chem B},
  Year                     = {2011},

  Month                    = {Oct},
  Number                   = {39},
  Pages                    = {11525--11529},
  Volume                   = {115},

  Abstract                 = {The three-color (BLN) 69-residue model protein was designed to exhibit frustrated folding. We investigate the energy landscape of this protein using disconnectivity graphs and compare it to a G? model, which is designed to reduce the frustration by removing all non-native attractive interactions. Finding the global minimum on a frustrated energy landscape is a good test of global optimization techniques, and we present calculations evaluating the performance of basin-hopping and genetic algorithms for this system. Comparisons are made with the widely studied 46-residue BLN protein. We show that the energy landscape of the 69-residue BLN protein contains several deep funnels, each of which corresponds to a different ?-barrel structure.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Oakley2011.pdf:PDF},
  Institution              = {School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {21866973},
  Timestamp                = {2011.11.28}
}

@Article{Offit2011,
  Title                    = {Personalized medicine: new genomics, old lessons},
  Author                   = {Offit, Kenneth},
  Journal                  = {Human genetics},
  Year                     = {2011},
  Number                   = {1},
  Pages                    = {3--14},
  Volume                   = {130},

  Owner                    = {ranjan},
  Publisher                = {Springer},
  Timestamp                = {2016.07.17}
}

@Article{Ohama2008,
  Title                    = {Evolving genetic code.},
  Author                   = {Takeshi Ohama and Yuji Inagaki and Yoshitaka Bessho and Syozo Osawa},
  Journal                  = {Proc Jpn Acad Ser B Phys Biol Sci},
  Year                     = {2008},
  Number                   = {2},
  Pages                    = {58--74},
  Volume                   = {84},

  Abstract                 = {In 1985, we reported that a bacterium, Mycoplasma capricolum, used a deviant genetic code, namely UGA, a "universal" stop codon, was read as tryptophan. This finding, together with the deviant nuclear genetic codes in not a few organisms and a number of mitochondria, shows that the genetic code is not universal, and is in a state of evolution. To account for the changes in codon meanings, we proposed the codon capture theory stating that all the code changes are non-disruptive without accompanied changes of amino acid sequences of proteins. Supporting evidence for the theory is presented in this review. A possible evolutionary process from the ancient to the present-day genetic code is also discussed.},
  Institution              = {Kochi University of Technology, Department of Environmental System Engineering, Kochi, Japan.},
  Keywords                 = {Amino Acid Sequence; Base Sequence; Codon; Evolution, Molecular; Genes, Bacterial; Genetic Code; Mycoplasma capricolum, genetics; RNA, Messenger, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {JST.JSTAGE/pjab/84.58},
  Pmid                     = {18941287},
  Timestamp                = {2011.09.16}
}

@Article{Ohta1996,
  Title                    = {Development of Neutral and Nearly Neutral Theories},
  Author                   = {Ohta and Gillespie},
  Journal                  = {Theor Popul Biol},
  Year                     = {1996},

  Month                    = {Apr},
  Number                   = {2},
  Pages                    = {128--142},
  Volume                   = {49},

  Abstract                 = {A short history of the major features of neutral theories of molecular evolution is presented. Emphasis is placed on the nearly neutral theory, as this version of the neutral theory has explained the widest range of phenomena. The shift of interest from protein to DNA evolution is chronicled, leading to the modern view that silent and replacement substitutions are responding to different evolutionary forces. However, the exact nature and magnitude of these forces remains controversial, as all current theoretical models suffer either from assumptions that are not quite realistic or from an inability to account readily for all phenomena. Although the gathering of sequence data has been the main effort of contemporary population genetics, further exploration of theoretical models of molecular evolution would provide a more coherent framework for data analysis.},
  Institution              = {National Institute of Genetics, , Mishima, , 411, Japan},
  Owner                    = {ranjan},
  Pii                      = {S0040580996900076},
  Pmid                     = {8813019},
  Timestamp                = {2011.04.27}
}

@Article{Ohta1973,
  Title                    = {Slightly deleterious mutant substitutions in evolution.},
  Author                   = {T. Ohta},
  Journal                  = {Nature},
  Year                     = {1973},

  Month                    = {Nov},
  Number                   = {5428},
  Pages                    = {96--98},
  Volume                   = {246},

  Keywords                 = {Alleles; Biological Evolution; Gene Frequency; Genes, Dominant; Genes, Recessive; Homozygote; Models, Biological; Mutation; Polymorphism, Genetic},
  Owner                    = {ranjan},
  Pmid                     = {4585855},
  Timestamp                = {2011.04.26}
}

@Article{Ohtsuki2009,
  Title                    = {Prelife catalysts and replicators.},
  Author                   = {Ohtsuki, Hisashi and Nowak, Martin A.},
  Journal                  = {Proc Biol Sci},
  Year                     = {2009},

  Month                    = {Nov},
  Number                   = {1674},
  Pages                    = {3783--3790},
  Volume                   = {276},

  Abstract                 = {Life is based on replication and evolution. But replication cannot be taken for granted. We must ask what there was prior to replication and evolution. How does evolution begin? We have proposed prelife as a generative system that produces information and diversity in the absence of replication. We model prelife as a binary soup of active monomers that form random polymers. 'Prevolutionary' dynamics can have mutation and selection prior to replication. Some sequences might have catalytic activity, thereby enhancing the rates of certain prelife reactions. We study the selection criteria for these prelife catalysts. Their catalytic efficiency must be above certain critical values. We find a maintenance threshold and an initiation threshold. The former is a linear function of sequence length, and the latter is an exponential function of sequence length. Therefore, it is extremely hard to select for prelife catalysts that have long sequences. We compare prelife catalysis with a 
simple model for replication. Assuming fast template-based elongation reactions, we can show that replicators have selection thresholds that are independent of their sequence length. Our calculation demonstrates the efficiency of replication and provides an explanation of why replication was selected over other forms of prelife catalysis.},
  Institution              = {PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan. ohtsuki.h.aa@m.titech.ac.jp},
  Keywords                 = {Biogenesis; Biological Evolution; Catalysis; Life; Models, Biological},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {rspb.2009.1136},
  Pmid                     = {19692408},
  Timestamp                = {2012.04.05}
}

@Article{Okazaki2008,
  Title                    = {Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms},
  Author                   = {Okazaki, Kei-ichi and Takada, Shoji},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2008},
  Number                   = {32},
  Pages                    = {11182--11187},
  Volume                   = {105},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2013.12.06}
}

@Article{Oldfield2005,
  Title                    = {Comparing and combining predictors of mostly disordered proteins.},
  Author                   = {Christopher J Oldfield and Yugong Cheng and Marc S Cortese and Celeste J Brown and Vladimir N Uversky and A. Keith Dunker},
  Journal                  = {Biochemistry},
  Year                     = {2005},

  Month                    = {Feb},
  Number                   = {6},
  Pages                    = {1989--2000},
  Volume                   = {44},

  Abstract                 = {Intrinsically disordered proteins and regions carry out varied and vital cellular functions. Proteins with disordered regions are especially common in eukaryotic cells, with a subset of these proteins being mostly disordered, e.g., with more disordered than ordered residues. Two distinct methods have been previously described for using amino acid sequences to predict which proteins are likely to be mostly disordered. These methods are based on the net charge-hydropathy distribution and disorder prediction score distribution. Each of these methods is reexamined, and the prediction results are compared herein. A new prediction method based on consensus is described. Application of the consensus method to whole genomes reveals that approximately 4.5\% of Yersinia pestis, 5\% of Escherichia coli K12, 6\% of Archaeoglobus fulgidus, 8\% of Methanobacterium thermoautotrophicum, 23\% of Arabidopsis thaliana, and 28\% of Mus musculus proteins are mostly disordered. The unexpectedly high 
frequency of mostly disordered proteins in eukaryotes has important implications both for large-scale, high-throughput projects and also for focused experiments aimed at determination of protein structure and function.},
  Institution              = {Molecular Kinetics, Inc., 6201 La Pas Trail, Suite 160, Indianapolis, Indiana 46268, USA.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Animals; Archaeal Proteins, chemistry/classification/metabolism; Bacterial Proteins, chemistry/classification/metabolism; Computational Biology, methods/statistics /&/ numerical data; Consensus Sequence; Crystallography, X-Ray; Databases, Protein; Entropy; False Positive Reactions; Humans; Mice; Models, Chemical; Predictive Value of Tests; Proteins, chemistry/classification/metabolism; ROC Curve; Static Electricity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {15697224},
  Timestamp                = {2013.08.24}
}

@Article{Oldfield2008,
  Title                    = {Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners.},
  Author                   = {Oldfield, Christopher J. and Meng, Jingwei and Yang, Jack Y. and Yang, Mary Qu and Uversky, Vladimir N. and Dunker, A Keith},
  Journal                  = {BMC Genomics},
  Year                     = {2008},
  Pages                    = {S1},
  Volume                   = {9 Suppl 1},

  Abstract                 = {Proteins are involved in many interactions with other proteins leading to networks that regulate and control a wide variety of physiological processes. Some of these proteins, called hub proteins or hubs, bind to many different protein partners. Protein intrinsic disorder, via diversity arising from structural plasticity or flexibility, provide a means for hubs to associate with many partners (Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN: Flexible Nets: The roles of intrinsic disorder in protein interaction networks. FEBS J 2005, 272:5129-5148).Here we present a detailed examination of two divergent examples: 1) p53, which uses different disordered regions to bind to different partners and which also has several individual disordered regions that each bind to multiple partners, and 2) 14-3-3, which is a structured protein that associates with many different intrinsically disordered partners. For both examples, three-dimensional structures of multiple complexes 
reveal that the flexibility and plasticity of intrinsically disordered protein regions as well as induced-fit changes in the structured regions are both important for binding diversity.These data support the conjecture that hub proteins often utilize intrinsic disorder to bind to multiple partners and provide detailed information about induced fit in structured regions.},
  Doi                      = {10.1186/1471-2164-9-S1-S1},
  Institution              = {Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, 410 W, 10th Street, Indianapolis, IN 46202, USA. cjoldfie@iupui.edu},
  Keywords                 = {14-3-3 Proteins, genetics/metabolism; Models, Molecular; Protein Binding; Protein Conformation; Signal Transduction, genetics; Tumor Suppressor Protein p53, genetics/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {1471-2164-9-S1-S1},
  Pmid                     = {18366598},
  Timestamp                = {2013.12.06}
}

@Article{Olsen1996,
  Title                    = {Lessons from an Archaeal genome: what are we learning from Methanococcus jannaschii?},
  Author                   = {G. J. Olsen and C. R. Woese},
  Journal                  = {Trends Genet},
  Year                     = {1996},

  Month                    = {Oct},
  Number                   = {10},
  Pages                    = {377--379},
  Volume                   = {12},

  Institution              = {U IL, Urbana},
  Keywords                 = {Animals; Archaea, genetics; Chromosomes, Bacterial; DNA Repair; Evolution; Genome, Bacterial; Genome, Human; Humans; Methanococcus, genetics; Mice; Saccharomyces cerevisiae, genetics},
  Owner                    = {ranjan},
  Pii                      = {0168-9525(96)30092-9},
  Pmid                     = {8909123},
  Timestamp                = {2009.11.28}
}

@Article{Onuchic1997,
  Title                    = {Theory of protein folding: the energy landscape perspective.},
  Author                   = {Onuchic, J. N. and Luthey-Schulten, Z. and Wolynes, P. G.},
  Journal                  = {Annu Rev Phys Chem},
  Year                     = {1997},
  Pages                    = {545--600},
  Volume                   = {48},

  Abstract                 = {The energy landscape theory of protein folding is a statistical description of a protein's potential surface. It assumes that folding occurs through organizing an ensemble of structures rather than through only a few uniquely defined structural intermediates. It suggests that the most realistic model of a protein is a minimally frustrated heteropolymer with a rugged funnel-like landscape biased toward the native structure. This statistical description has been developed using tools from the statistical mechanics of disordered systems, polymers, and phase transitions of finite systems. We review here its analytical background and contrast the phenomena in homopolymers, random heteropolymers, and protein-like heteropolymers that are kinetically and thermodynamically capable of folding. The connection between these statistical concepts and the results of minimalist models used in computer simulations is discussed. The review concludes with a brief discussion of how the theory helps 
in the interpretation of results from fast folding experiments and in the practical task of protein structure prediction.},
  Doi                      = {10.1146/annurev.physchem.48.1.545},
  Institution              = {Department of Physics, University of California at San Diego, La Jolla 92093-0319, USA.},
  Keywords                 = {Amino Acid Sequence; Computer Simulation; Models, Molecular; Molecular Sequence Data; Polymers; Protein Folding; Sequence Homology, Amino Acid; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9348663},
  Timestamp                = {2014.02.24}
}

@Article{Oparin1976,
  Title                    = {Evolution of the concepts of the origin of life, 1924-1974.},
  Author                   = {Oparin, A. I.},
  Journal                  = {Orig Life},
  Year                     = {1976},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {3--8},
  Volume                   = {7},

  Keywords                 = {Biogenesis; Nucleic Acids; Proteins; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {967402},
  Timestamp                = {2012.04.05}
}

@Article{Oparin1924,
  Title                    = {Proiskhozhdenie zhizny.},
  Author                   = {Oparin, A. I.},
  Journal                  = {Izd. Moskovski Rabochii, Moscow},
  Year                     = {1924},

  Owner                    = {ranjan},
  Timestamp                = {2012.04.06}
}

@Article{Oro1990,
  Title                    = {The origin and early evolution of life on Earth.},
  Author                   = {Or\'{o}, J. and Miller, S. L. and Lazcano, A.},
  Journal                  = {Annu Rev Earth Planet Sci},
  Year                     = {1990},
  Pages                    = {317--356},
  Volume                   = {18},

  Abstract                 = {We do not have a detailed knowledge of the processes that led to the appearance of life on Earth. In this review we bring together some of the most important results that have provided insights into the cosmic and primitive Earth environments, particularly those environments in which life is thought to have originated. To do so, we first discuss the evidence bearing on the antiquity of life on our planet and the prebiotic significance of organic compounds found in interstellar clouds and in primitive solar system bodies such as comets, dark asteroids, and carbonaceous chondrites. This is followed by a discussion on the environmental models of the Hadean and early Archean Earth, as well as on the prebiotic formation of organic monomers and polymers essential to life. We then consider the processes that may have led to the appearance in the Archean of the first cells, and how these processes may have affected the early steps of biological evolution. Finally, the significance of 
these results to the study of the distribution of life in the Universe is discussed.},
  Institution              = {U CA at San Diego, La Jolla, Dept Chem},
  Keywords                 = {Atmosphere; Bacteria; Biogenesis; Biological Evolution; Earth (Planet); Evolution, Molecular; Fossils; Meteoroids; Paleontology; Solar System},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {11538678},
  Timestamp                = {2012.04.05}
}

@Article{Orengo2005,
  Title                    = {Protein families and their evolution-a structural perspective.},
  Author                   = {Christine A Orengo and Janet M Thornton},
  Journal                  = {Annu Rev Biochem},
  Year                     = {2005},
  Pages                    = {867--900},
  Volume                   = {74},

  Abstract                 = {We can now assign about two thirds of the sequences from completed genomes to as few as 1400 domain families for which structures are known and thus more ancient evolutionary relationships established. About 200 of these domain families are common to all kingdoms of life and account for nearly 50\% of domain structure annotations in the genomes. Some of these domain families have been very extensively duplicated within a genome and combined with different domain partners giving rise to different multidomain proteins. The ways in which these domain combinations evolve tend to be specific to the organism so that less than 15\% of the protein families found within a genome appear to be common to all kingdoms of life. Recent analyses of completed genomes, exploiting the structural data, have revealed the extent to which duplication of these domains and modifications of their functions can expand the functional repertoire of the organism, contributing to increasing complexity.},
  File                     = {Orengo2005.pdf:pdfs/Orengo2005.pdf:PDF},
  Institution              = {Department of Biochemistry and Molecular Biology, University College, London WC1E 6BT, United Kingdom. orengo@biochemistry.ucl.ac.uk},
  Keywords                 = {Animals; Bacterial Proteins, chemistry/classification/genetics; Databases, Protein; Evolution, Molecular; Genome; Humans; Immunoglobulins, chemistry/classification/genetics; Models, Molecular; Protein Folding; Protein Structure, Tertiary; Proteins, chemistry/classification/genetics; Proteome},
  Owner                    = {ranjan},
  Pmid                     = {15954844},
  Timestamp                = {2009.09.14}
}

@Article{Orgel1994,
  Title                    = {The origin of life on the earth.},
  Author                   = {Orgel, L. E.},
  Journal                  = {Sci Am},
  Year                     = {1994},

  Month                    = {Oct},
  Number                   = {4},
  Pages                    = {76--83},
  Volume                   = {271},

  Abstract                 = {Growing evidence supports the idea that the emergence of catalytic RNA was a crucial early step. How that RNA came into being remains unknown.},
  Institution              = {U CA, San Diego},
  Keywords                 = {Animals; Base Sequence; Biogenesis; Earth (Planet); Humans; Molecular Sequence Data; RNA, Catalytic; RNA, biosynthesis},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {7524147},
  Timestamp                = {2012.04.05}
}

@Article{Orosz2011,
  Title                    = {Proteins without 3D structure: definition, detection and beyond},
  Author                   = {Orosz, Ferenc and Ov{\'a}di, Judit},
  Journal                  = {Bioinformatics},
  Year                     = {2011},
  Number                   = {11},
  Pages                    = {1449--1454},
  Volume                   = {27},

  Owner                    = {ranjan},
  Publisher                = {Oxford Univ Press},
  Timestamp                = {2013.11.18}
}

@Article{Osawa1992,
  Title                    = {Recent evidence for evolution of the genetic code.},
  Author                   = {S. Osawa and T. H. Jukes and K. Watanabe and A. Muto},
  Journal                  = {Microbiol Rev},
  Year                     = {1992},

  Month                    = {Mar},
  Number                   = {1},
  Pages                    = {229--264},
  Volume                   = {56},

  Abstract                 = {The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (
arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.},
  Institution              = {U CA, Berkeley},
  Keywords                 = {Base Sequence; Biological Evolution; Cell Nucleus, chemistry; Codon, classification; Genetic Code; Mitochondria, chemistry; Molecular Sequence Data; Nucleic Acid Conformation},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {1579111},
  Timestamp                = {2011.09.16}
}

@Article{Overby2008,
  Title                    = {Insights into bunyavirus architecture from electron cryotomography of Uukuniemi virus},
  Author                   = {Overby,A.K. and Pettersson, R.F. and Gr\"unewald, K. and Huiskonen, J.T.},
  Journal                  = PNAS,
  Year                     = {2008},
  Number                   = {7},
  Pages                    = {2375-2379},
  Volume                   = {105},

  File                     = {Overby2008.pdf:pdfs/Overby2008.pdf:PDF}
}

@Article{Owczarek2008,
  Title                    = {Scaling of the atmosphere of self-avoiding walks},
  Author                   = {Owczarek, AL and Prellberg, Thomas},
  Journal                  = {Journal of Physics A: Mathematical and Theoretical},
  Year                     = {2008},
  Number                   = {37},
  Pages                    = {375004},
  Volume                   = {41},

  Owner                    = {ranjan},
  Publisher                = {IOP Publishing},
  Timestamp                = {2014.08.31}
}

@Article{Jagarlapudi1996,
  Title                    = {Even-odd carbon atom disparity},
  Author                   = {JAGARLAPUDI A. R. P. and SARMA, ASHWINI NANGIA and GAUTAM R. DESIRAJU and ENGELBERT ZASS and JACK D. DUNITZ},
  Journal                  = {Nature},
  Year                     = {1996},
  Pages                    = {320},
  Volume                   = {384},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Padilla2001,
  Title                    = {Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments.},
  Author                   = {Padilla,J.E. and Colovos,C. and Yeates,T.O.},
  Journal                  = PNAS,
  Year                     = {2001},
  Number                   = {5},
  Pages                    = {2217--2221},
  Volume                   = {98},

  File                     = {Padilla2001.pdf:pdfs/Padilla2001.pdf:PDF}
}

@Article{Pagel1999,
  Title                    = {Inferring the historical patterns of biological evolution.},
  Author                   = {M. Pagel},
  Journal                  = {Nature},
  Year                     = {1999},

  Month                    = {Oct},
  Number                   = {6756},
  Pages                    = {877--884},
  Volume                   = {401},

  Abstract                 = {Phylogenetic trees describe the pattern of descent amongst a group of species. With the rapid accumulation of DNA sequence data, more and more phylogenies are being constructed based upon sequence comparisons. The combination of these phylogenies with powerful new statistical approaches for the analysis of biological evolution is challenging widely held beliefs about the history and evolution of life on Earth.},
  Institution              = {School of Animal and Microbial Sciences, University of Reading, Whiteknights, UK.},
  Keywords                 = {Animals; Biological Evolution; Brain, anatomy /&/ histology; Evolution, Molecular; Humans; Likelihood Functions; Mammals; Models, Biological; Models, Statistical; Orthomyxoviridae, genetics; Phylogeny; Proteins, genetics; Ribonucleases, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {10553904},
  Timestamp                = {2012.03.11}
}

@Article{Pagel1997,
  Title                    = {Inferring evolutionary processes from phylogenies},
  Author                   = {Mark Pagel},
  Journal                  = {Zoologica Scripta},
  Year                     = {1997},
  Number                   = {4},
  Pages                    = {331--348},
  Volume                   = {26},

  Owner                    = {ranjan},
  Timestamp                = {2012.03.13}
}

@Article{Pagel2006,
  Title                    = {Large punctuational contribution of speciation to evolutionary divergence at the molecular level.},
  Author                   = {Mark Pagel and Chris Venditti and Andrew Meade},
  Journal                  = {Science},
  Year                     = {2006},

  Month                    = {Oct},
  Number                   = {5796},
  Pages                    = {119--121},
  Volume                   = {314},

  Abstract                 = {A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the time of speciation. We found that approximately 22\% of substitutional changes at the DNA level can be attributed to punctuational evolution, and the remainder accumulates from background gradual divergence. Punctuational effects occur at more than twice the rate in plants and fungi than in animals, but the proportion of total divergence attributable to punctuational change does not vary among these groups. Punctuational changes cause departures from a clock-like tempo of evolution, suggesting that they should be accounted for in deriving dates from phylogenies. Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Pagel2006.pdf:PDF},
  Institution              = {School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK. m.pagel@rdg.ac.uk},
  Keywords                 = {Animals; Base Sequence; Bayes Theorem; DNA, Fungal, genetics; DNA, Plant, genetics; DNA, genetics; Evolution, Molecular; Founder Effect; Fungi, classification/genetics; Genetic Speciation; Genetic Variation; Likelihood Functions; Mathematics; Models, Statistical; Mutation; Phylogeny; Plants, classification/genetics; Sequence Alignment},
  Owner                    = {ranjan},
  Pii                      = {314/5796/119},
  Pmid                     = {17023657},
  Timestamp                = {2011.04.26}
}

@Article{Papoian2003,
  Title                    = {The physics and bioinformatics of binding and folding-an energy landscape perspective.},
  Author                   = {Papoian, Garegin A. and Wolynes, Peter G.},
  Journal                  = {Biopolymers},
  Year                     = {2003},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {333--349},
  Volume                   = {68},

  Abstract                 = {It has been recognized in the last few years that unstructured proteins play an important role in biological organisms, often participating in signal transduction, transcriptional regulation, and a variety of other regulatory activities. Various hypotheses have been put forward for the ubiquity of the unfolded state; rapid turnover, faster or more specific binding kinetics, multifunctionality may all possibly explain apparent ubiquitousness of unfolded proteins in eukaryotic cells. In this paper we extend the energy landscape theory of protein folding to construct an analytical model of how binding and folding are coupled thermodynamically when the energy landscape is partially rugged. To deduce the parameters that enter the theory, which is based on Generalized Random Energy Model, we have analyzed in a bioinformatic sense a large structural database of more than 500 protein complexes. We find that Miyazawa-Jernigan contact potential shows similar energy gaps for folding for 
both hydrophobic and hydrophilic proteins, but that for binding contacts hydrophobic interfaces turn out to be funneled while hydrophilic ones are antifunneled. This suggests evolution has found a mechanism for avoiding frustration between folding and binding by making use of indirect water-mediated interactions. By juxtaposing the monomeric protein folding free energy profile in the protein complex database with another database consisting of only well-folded monomers, we estimate that at least 15\% of monomers in the former database are unfolded in the absence of partner protein interface interactions. When employing the parameters characteristic of these unfolded monomers to construct binding/folding phase diagrams, we find that these monomers would indeed fold if sufficiently stabilizing binding contacts, consistent with that fold, are formed.},
  Doi                      = {10.1002/bip.10286},
  Institution              = { Biochemistry, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0371, USA.},
  Keywords                 = {Computational Biology, methods; Databases, Protein; Models, Molecular; Physical Phenomena; Physics; Protein Binding; Protein Folding},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {12601793},
  Timestamp                = {2014.02.24}
}

@Article{Pareek2011,
  Title                    = {Sequencing technologies and genome sequencing},
  Author                   = {Pareek, Chandra Shekhar and Smoczynski, Rafal and Tretyn, Andrzej},
  Journal                  = {Journal of applied genetics},
  Year                     = {2011},
  Number                   = {4},
  Pages                    = {413--435},
  Volume                   = {52},

  Owner                    = {ranjan},
  Publisher                = {Springer},
  Timestamp                = {2016.07.17}
}

@Article{Park2007,
  Title                    = {Energetics-based protein profiling on a proteomic scale: identification of proteins resistant to proteolysis.},
  Author                   = {Chiwook Park and Sharleen Zhou and Jacqueline Gilmore and Susan Marqusee},
  Journal                  = {J Mol Biol},
  Year                     = {2007},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {1426--1437},
  Volume                   = {368},

  Abstract                 = {Native states of proteins are flexible, populating more than just the unique native conformation. The energetics and dynamics resulting from this conformational ensemble are inherently linked to protein function and regulation. Proteolytic susceptibility is one feature determined by this conformational energy landscape. As an attempt to investigate energetics of proteins on a proteomic scale, we challenged the Escherichia coli proteome with extensive proteolysis and determined which proteins, if any, have optimized their energy landscape for resistance to proteolysis. To our surprise, multiple soluble proteins survived the challenge. Maltose binding protein, a survivor from thermolysin digestion, was characterized by in vitro biophysical studies to identify the physical origin of proteolytic resistance. This experimental characterization shows that kinetic stability is responsible for the unusual resistance in maltose binding protein. The biochemical functions of the identified 
survivors suggest that many of these proteins may have evolved extreme proteolytic resistance because of their critical roles under stressed conditions. Our results suggest that under functional selection proteins can evolve extreme proteolysis resistance by modulating their conformational energy landscapes without the need to invent new folds, and that proteins can be profiled on a proteomic scale according to their energetic properties by using proteolysis as a structural probe.},
  Institution              = {Department of Molecular and Cell Biology and QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-3206, USA.},
  Keywords                 = {Carrier Proteins, chemistry/metabolism; Escherichia coli Proteins, chemistry/metabolism; Hydrolysis; Models, Molecular; Molecular Sequence Data; Protein Conformation; Proteome, analysis; Thermodynamics; Thermolysin, metabolism},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(07)00305-1},
  Pmid                     = {17400245},
  Timestamp                = {2010.05.02}
}

@Article{Patil2010,
  Title                    = {Hub promiscuity in protein-protein interaction networks},
  Author                   = {Patil, Ashwini and Kinoshita, Kengo and Nakamura, Haruki},
  Journal                  = {International journal of molecular sciences},
  Year                     = {2010},
  Number                   = {4},
  Pages                    = {1930--1943},
  Volume                   = {11},

  Owner                    = {ranjan},
  Publisher                = {Molecular Diversity Preservation International},
  Timestamp                = {2013.12.06}
}

@Article{Patil2006,
  Title                    = {Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks},
  Author                   = {Patil, Ashwini and Nakamura, Haruki},
  Journal                  = {FEBS letters},
  Year                     = {2006},
  Number                   = {8},
  Pages                    = {2041--2045},
  Volume                   = {580},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.12.06}
}

@Article{Paul2011,
  Title                    = {Peptoid atropisomers.},
  Author                   = {Paul, Bishwajit and Butterfoss, Glenn L. and Boswell, Mikki G. and Renfrew, P Douglas and Yeung, Fanny G. and Shah, Neel H. and Wolf, Christian and Bonneau, Richard and Kirshenbaum, Kent},
  Journal                  = {J Am Chem Soc},
  Year                     = {2011},

  Month                    = {Jul},
  Number                   = {28},
  Pages                    = {10910--10919},
  Volume                   = {133},

  Abstract                 = {We report the isolation of N-aryl peptoid oligomers that adopt chiral folds, despite the absence of chiral centers. Peptoid monomers incorporating ortho-substituted N-aryl side chains are identified that exhibit axial chirality. We observe significant energy barriers to rotation about the stereogenic carbon-nitrogen bond, allowing chromatographic purification of stable atropisomeric forms. We study the atropisomerism of N-aryl peptoid oligomers by computational modeling, NMR, X-ray crystallography, dynamic HPLC, and circular dichroism. The results demonstrate a new approach to promote the conformational ordering of this important class of foldamer compounds.},
  Institution              = {Department of Chemistry, New York University, New York, New York 10003, USA.},
  Keywords                 = {Chromatography, High Pressure Liquid; Circular Dichroism; Crystallography, X-Ray; Dimerization; Magnetic Resonance Spectroscopy; Models, Molecular; Peptoids, chemistry; Protein Conformation; Rotation; Stereoisomerism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {21634437},
  Timestamp                = {2012.08.26}
}

@Article{Pauling1940,
  Title                    = {A Theory of the Structure and Process of Formation of Antibodies*},
  Author                   = {Pauling, Linus},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {1940},
  Number                   = {10},
  Pages                    = {2643--2657},
  Volume                   = {62},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2013.06.30}
}

@Article{Pauling1951a,
  Title                    = {The pleated sheet, a new layer configuration of polypeptide chains},
  Author                   = {Pauling, Linus and Corey, Robert B},
  Journal                  = {Proceedings of the National Academy of Sciences of the United States of America},
  Year                     = {1951},
  Number                   = {5},
  Pages                    = {251},
  Volume                   = {37},

  Owner                    = {ranjan},
  Publisher                = {National Academy of Sciences},
  Timestamp                = {2013.11.11}
}

@Article{Pauling1951b,
  Title                    = {Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets},
  Author                   = {Pauling, Linus and Corey, Robert B},
  Journal                  = {Proceedings of the National Academy of Sciences of the United States of America},
  Year                     = {1951},
  Number                   = {11},
  Pages                    = {729},
  Volume                   = {37},

  Owner                    = {ranjan},
  Publisher                = {National Academy of Sciences},
  Timestamp                = {2015.11.15}
}

@Article{Pauling1951,
  Title                    = {The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain},
  Author                   = {Pauling, Linus and Corey, Robert B and Branson, Herman R},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {1951},
  Number                   = {4},
  Pages                    = {205--211},
  Volume                   = {37},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2013.11.10}
}

@Article{Pei2003,
  Title                    = {Using protein design for homology detection and active site searches.},
  Author                   = {Jimin Pei and Nikolay V Dokholyan and Eugene I Shakhnovich and Nick V Grishin},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2003},

  Month                    = {Sep},
  Number                   = {20},
  Pages                    = {11361--11366},
  Volume                   = {100},

  Abstract                 = {We describe a method of designing artificial sequences that resemble naturally occurring sequences in terms of their compatibility with a template structure and its functional constraints. The design procedure is a Monte Carlo simulation of amino acid substitution process. The selective fixation of substitutions is dictated by a simple scoring function derived from the template structure and a multiple alignment of its homologs. Designed sequences represent an enlargement of sequence space around native sequences. We show that the use of designed sequences improves the performance of profile-based homology detection. The difference in position-specific conservation between designed sequences and native sequences is helpful for prediction of functionally important residues. Our sequence selection criteria in evolutionary simulations introduce amino acid substitution rate variation among sites in a natural way, providing a better model to test phylogenetic methods.},
  Institution              = {Department of Biochemistry and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.},
  Keywords                 = {Binding Sites; Evolution, Molecular; Models, Chemical; Proteins, chemistry/metabolism},
  Owner                    = {ranjan},
  Pii                      = {2034878100},
  Pmid                     = {12975528},
  Timestamp                = {2009.12.05}
}

@Article{Perlstein2007,
  Title                    = {Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations.},
  Author                   = {Ethan O Perlstein and Eric J Deeds and Orr Ashenberg and Eugene I Shakhnovich and Stuart L Schreiber},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2007},

  Month                    = {Jun},
  Number                   = {25},
  Pages                    = {10553--10558},
  Volume                   = {104},

  Abstract                 = {Studies of the role of sex in evolution typically involve a longitudinal comparison of a single ancestor to several intermediate descendants and to one terminally evolved descendant after many generations of adaptation under a given selective regime. Here we take a complementary, statistical approach to sex in evolution, by describing the distribution of phenotypic similarity in a population of yeast F1 meiotic recombinants. By applying graph theory to fitness measurements of thousands of Saccharomyces cerevisiae recombinants treated with 10 mechanistically distinct, growth-inhibitory small-molecule perturbagens (SMPs), we show that the network of phenotypic similarity among F1 recombinants exhibits a scale-free degree distribution. F1 recombinants are often phenotypically unique and sometimes exceptional, and their fitness strengths are unevenly distributed across the 10 compound treatments. By contrast, highly phenotypically similar F1 recombinants constitute failing hubs that 
display below-average fitness across all compound treatments and are candidate substrates for purifying selection. Comparison of the F1 generation with the parental strains reveals that (i) there is a specialist more fit in any given single condition than any of the parents but (ii) only rarely are there generalists that exhibit greater fitness than both parental strains across a majority of conditions. This analysis allows us to evaluate and to gain better theoretical understanding of the costs and benefits of sex in the F1 generation.},
  Institution              = {Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. perlst@fas.harvard.edu},
  Keywords                 = {Genetics, Population; Meiosis; Models, Theoretical; Molecular Weight; Phenotype; Recombination, Genetic; Saccharomyces cerevisiae, drug effects/genetics; Spores, Fungal, drug effects/growth /&/ development; Xenobiotics, chemistry/pharmacology},
  Owner                    = {ranjan},
  Pii                      = {0704037104},
  Pmid                     = {17566105},
  Timestamp                = {2009.12.05}
}

@Article{Perutz1951,
  Title                    = {New X-Ray Evidence on the Configuration of Polypeptide Chains: Polypeptide Chains in Poly-gamma-benzyl-L-glutamate, Keratin and H{\ae}moglobin},
  Author                   = {Perutz, MFf},
  Journal                  = {Nature},
  Year                     = {1951},
  Pages                    = {1053--1054},
  Volume                   = {167},

  Owner                    = {ranjan},
  Timestamp                = {2013.11.12}
}

@Article{Peters2009,
  Title                    = {Competing nucleation pathways in a mixture of oppositely charged colloids: Out-of-equilibrium nucleation revisited},
  Author                   = {Peters, Baron},
  Journal                  = {The Journal of chemical physics},
  Year                     = {2009},
  Number                   = {24},
  Pages                    = {244103},
  Volume                   = {131},

  Owner                    = {ranjan},
  Publisher                = {AIP Publishing},
  Timestamp                = {2015.04.20}
}

@Article{Peters2012,
  Title                    = {Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection},
  Author                   = {Peters, Jan H and de Groot, Bert L},
  Journal                  = {PLoS computational biology},
  Year                     = {2012},
  Number                   = {10},
  Pages                    = {e1002704},
  Volume                   = {8},

  Owner                    = {ranjan},
  Publisher                = {Public Library of Science},
  Timestamp                = {2013.11.17}
}

@Article{Peterson2009,
  Title                    = {Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment.},
  Author                   = {Eric L Peterson and Jan? Kondev and Julie A Theriot and Rob Phillips},
  Journal                  = {Bioinformatics},
  Year                     = {2009},

  Month                    = {Jun},
  Number                   = {11},
  Pages                    = {1356--1362},
  Volume                   = {25},

  Abstract                 = {MOTIVATION: Many proteins with vastly dissimilar sequences are found to share a common fold, as evidenced in the wealth of structures now available in the Protein Data Bank. One idea that has found success in various applications is the concept of a reduced amino acid alphabet, wherein similar amino acids are clustered together. Given the structural similarity exhibited by many apparently dissimilar sequences, we undertook this study looking for improvements in fold recognition by comparing protein sequences written in a reduced alphabet. RESULTS: We tested over 150 of the amino acid clustering schemes proposed in the literature with all-versus-all pairwise sequence alignments of sequences in the Distance mAtrix aLIgnment database. We combined several metrics from information retrieval popular in the literature: mean precision, area under the Receiver Operating Characteristic curve and recall at a fixed error rate and found that, in contrast to previous work, reduced alphabets 
in many cases outperform full alphabets. We find that reduced alphabets can perform at a level comparable to full alphabets in correct pairwise alignment of sequences and can show increased sensitivity to pairs of sequences with structural similarity but low-sequence identity. Based on these results, we hypothesize that reduced alphabets may also show performance gains with more sophisticated methods such as profile and pattern searches. AVAILABILITY: A table of results as well as the substitution matrices and residue groupings from this study can be downloaded from (http://www.rpgroup.caltech.edu/publications/supplements/alphabets).},
  File                     = {Peterson2009.pdf:pdfs/Peterson2009.pdf:PDF},
  Institution              = {Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Amino Acids, chemistry; Computational Biology, methods; Databases, Protein; Protein Conformation; Protein Folding; Sequence Alignment, methods; Sequence Analysis, Protein, methods},
  Owner                    = {ranjan},
  Pii                      = {btp164},
  Pmid                     = {19351620},
  Timestamp                = {2009.10.03}
}

@Article{Pink1975,
  Title                    = {The even--odd effect in liquid crystals. A simple model},
  Author                   = {D. A. Pink},
  Journal                  = {J. Chem. Phys.},
  Year                     = {1975},
  Pages                    = {2533--2539},
  Volume                   = {63},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Pizzarello2012,
  Title                    = {Large enantiomeric excesses in primitive meteorites and the diverse effects of water in cosmochemical evolution.},
  Author                   = {Pizzarello, Sandra and Schrader, Devin L. and Monroe, Adam A. and Lauretta, Dante S.},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2012},

  Month                    = {Jul},
  Number                   = {30},
  Pages                    = {11949--11954},
  Volume                   = {109},

  Abstract                 = {Carbonaceous chondrites are meteoritic fragments of asteroids that avoided the geological reprocessing of larger planets and allow laboratory probing of early solar-nebula materials. Among these, Renazzo-type (CR) chondrites found in Antarctica appear remarkably pristine and are distinguished by abundant organic materials and water-soluble molecules such as amino acids and ammonia. We present a comprehensive analysis of the organic composition of selected CR meteorites of different petrographic classification and compare compounds' abundance and distribution as they may relate to asteroidal aqueous processing and concomitant evolution of the mineral phases. We found that several CR compounds such as amino acids and sugar alcohols are fully represented in stones with no or minimal water exposure indicating a formation that, if solar, preceded parent body processes. The most pristine CRs also revealed natal enantiomeric excesses (ee) of up to 60\%, much larger than ever recorded. 
However, aqueous alteration appears to affect CR soluble organic composition and abundances, in particular some diastereomeric amino acids may gauge its extent by the consequent racemization of their ee.},
  Doi                      = {10.1073/pnas.1204865109},
  Institution              = {Arizona State University, Department of Chemistry and Biochemistry, Tempe, AZ 85287-1604, USA. pizzar@asu.edu},
  Keywords                 = {Amino Acids, analysis; Antarctic Regions; Evolution, Chemical; Gas Chromatography-Mass Spectrometry; Meteoroids; Sugar Alcohols, analysis; Water, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {1204865109},
  Pmid                     = {22778439},
  Timestamp                = {2014.02.25}
}

@Article{Plankensteiner2005,
  Title                    = {Catalytically increased prebiotic peptide formation: ditryptophan, dilysine, and diserine.},
  Author                   = {Kristof Plankensteiner and Hannes Reiner and Bernd M Rode},
  Journal                  = {Orig Life Evol Biosph},
  Year                     = {2005},

  Month                    = {Oct},
  Number                   = {5},
  Pages                    = {411--419},
  Volume                   = {35},

  Abstract                 = {"Mutual" amino acid catalysis of glycine on the formation of ditryptophan, dilysine, and diserine in the prebiotically relevant Salt-Induced Peptide Formation (SIPF) Reaction was investigated varying the starting concentration and chirality of the educt amino acid, and analyzing the increase of yield resulting from this catalytic effect. Our results show the possibility of an amplified diverse pool of peptides being available for chemical evolution of larger peptides and proteins using also these more complicated amino acids for the evolution of more complex functions in future biochemical cycles and thus for the emergence of life. Catalytic effects are especially high in the case of serine, the most basic amino acid of the three, but are also significant for the other two examples investigated in the present work. Besides that, especially for serine, but also in the case of tryptophan, differences in catalytic yield increase according to the chiral form of the amino acid used 
could be observed.},
  Institution              = {Division of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.},
  Keywords                 = {Amino Acids, chemistry; Biogenesis; Catalysis; Chromatography, High Pressure Liquid; Dipeptides, chemical synthesis/chemistry; Evolution, Chemical; Serine, chemistry; Tryptophan, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {16231205},
  Timestamp                = {2011.08.12}
}

@Article{Plaxco1998,
  Title                    = {Simplified proteins: minimalist solutions to the 'protein folding problem'.},
  Author                   = {K. W. Plaxco and D. S. Riddle and V. Grantcharova and D. Baker},
  Journal                  = {Curr Opin Struct Biol},
  Year                     = {1998},

  Month                    = {Feb},
  Number                   = {1},
  Pages                    = {80--85},
  Volume                   = {8},

  Abstract                 = {Recent research has suggested that stable, native proteins may be encoded by simple sequences of fewer than the full set of 20 proteogenic amino acids. Studies of the ability of simple amino acid sequences to encode stable, topologically complex, native conformations and to fold to these conformations in a biologically relevant time frame have provided insights into the sequence determinants of protein structure and folding kinetics. They may also have important implications for protein design and for theories of the origins of protein synthesis itself.},
  File                     = {Plaxco1998.pdf:pdfs/Plaxco1998.pdf:PDF},
  Institution              = {Department of Biochemistry, University of Washington, Seattle 98195, USA. kwp@elina.bchem.washington.edu},
  Keywords                 = {Amino Acid Sequence; Kinetics; Models, Molecular; Protein Biosynthesis; Protein Conformation; Protein Engineering; Protein Folding; Protein Structure, Secondary; Proteins, chemistry},
  Owner                    = {ranjan},
  Pii                      = {S0959-440X(98)80013-4},
  Pmid                     = {9519299},
  Timestamp                = {2009.10.03}
}

@Article{Plestenjak1999,
  Title                    = {An Algorithm for Drawing Planar Graphs},
  Author                   = {Plestenjak,B.},
  Journal                  = {Softw. Pract. Exper.},
  Year                     = {1999},
  Pages                    = {973-984},
  Volume                   = {29},

  Owner                    = {ranjan},
  Timestamp                = {2009.08.12}
}

@Article{Pohl2012,
  Title                    = {Exploiting diverse stereochemistry of $\beta$-amino acids: toward a rational design of sheet-forming $\beta$-peptide systems.},
  Author                   = {Pohl, G{\'{a}}bor and Beke-Somfai, Tam{\'{a}}s and Csizmadia, Imre G. and Perczel, Andr{\'{a}}s},
  Journal                  = {Amino Acids},
  Year                     = {2012},

  Month                    = {Aug},
  Number                   = {2},
  Pages                    = {735--749},
  Volume                   = {43},

  Abstract                 = {Due to the two methylene groups in their backbone, β-amino acids can adopt numerous secondary structures, including helices, sheets and nanotubes. Chirality introduced by the additional side chains can significantly influence the folding preference of β-peptides composed of chiral β-amino acids. However, only conceptual suggestions are present in the literature about the effect of chirality on folding preferences. Summarizing both the experimental and computational results, Seebach (Chem Biodivers 1:1111-1240, 2004) has proposed the first selection rule on the effect of side chain chirality, on the folding preference of β-peptides. In order to extend and fine-tune the aforementioned predictions of Seebach, we have investigated its validity to the novel type of apolar sheet proposed recently (Pohl et al. in J Phys Chem B 114:9338-9348, 2010). In order to facilitate the rational design of sheet-like structures, a systematic study on the effect of chirality on "apolar" sheet 
stability is presented on disubstituted [HCO-β-Ala-β(2,3)-hAla-β-Ala-NH(2)](2) model peptides calculated at the M05-2X/6-311++G(d,p)//M05-2X/6-31G(d) and B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) levels of theory both in vacuum and in polar and apolar solvents. In addition, both types of "apolar" sheets were investigated; the one with two strands of identical (AA) and enantiomeric (AB) backbone structure. Our results show that heterochirally disubstituted sheets have the greatest preference for sheet formation (ΔG ~ -11 kcal mol(-1)). However, in contrast to Seebach's predictions, "homochiral disubstitution" itself does not necessarily disrupt the sheet structure, rather it could result stable fold (ΔG ~ -5 kcal mol(-1)). Results indicate that both the methyl group orientation and the local conformational effect of substitution affects sheet stability, as point chirality was found to have influence only on the backbone torsional angles. These results enabled us to extend and generalize Seebach's predictions and to 
propose a more general and accurate "rule of thumb" describing the effect of chirality on sheet stability. This offers an easy-to-use summary on how to design β-peptide sheet structures. We conclude that heterochirally disubstituted models are the best candidates for sheet formation, if the two strands are substituted in a way to create identical torsional angle sets on the two backbones for ideal hydrogen-bonding pattern. With adequately selected side chains, homochirally disubtituted derivatives may also form sheet structures, and the position of methyl groups would prevent assembly of more than two strands making it ideal to create hairpins.},
  Doi                      = {10.1007/s00726-011-1124-7},
  Institution              = {Department of Organic Chemistry, Eötvös Loránd University, Budapest 1117, Hungary.},
  Keywords                 = {Computer Simulation; Heptanes, chemistry; Hydrogen Bonding; Models, Molecular; Oligopeptides, chemistry; Protein Folding; Protein Multimerization; Protein Stability; Protein Structure, Secondary; Solvents, chemistry; Stereoisomerism; Thermodynamics; Water, chemistry; beta-Alanine, analogs /&/ derivatives/chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {22057667},
  Timestamp                = {2014.04.26}
}

@Article{Povolotskaya2010,
  Title                    = {Sequence space and the ongoing expansion of the protein universe.},
  Author                   = {Inna S Povolotskaya and Fyodor A Kondrashov},
  Journal                  = {Nature},
  Year                     = {2010},

  Month                    = {Jun},
  Number                   = {7300},
  Pages                    = {922--926},
  Volume                   = {465},

  Abstract                 = {The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: approximately 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast 
majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, approximately 3.5 x 10(9) yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.},
  Institution              = {Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Calle Dr Aiguader 88, Barcelona Biomedical Research Park Building, 08003 Barcelona, Spain.},
  Keywords                 = {Amino Acid Sequence; Amino Acid Substitution; Amino Acids, chemistry; Evolution, Molecular; Genetic Variation; Molecular Sequence Data; Mutation; Prokaryotic Cells; Protein Structure, Secondary; Proteins, chemistry; Selection, Genetic, genetics; Sequence Analysis, Protein; Sequence Homology, Amino Acid},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nature09105},
  Pmid                     = {20485343},
  Timestamp                = {2011.09.15}
}

@Article{Prevelige1998,
  Title                    = {Inhibiting virus-capsid assembly by altering the polymerisation pathway.},
  Author                   = {Prevelige Jr., P.E.},
  Journal                  = {Trends Biotechnol.},
  Year                     = {1998},
  Number                   = {2},
  Pages                    = {61-65},
  Volume                   = {16},

  File                     = {Prevelige1998.pdf:pdfs/Prevelige1998.pdf:PDF}
}

@Book{Pritychenko2012,
  Title                    = {Stellar Nucleosynthesis Nuclear Data Mining},
  Author                   = {Pritychenko, Boris},
  Publisher                = {InTech},
  Year                     = {2012},
  Month                    = {Mar},

  Doi                      = {10.5772/34451},
  ISBN                     = {978-953-51-0473-5},
  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Ptitsyn1995a,
  Title                    = {How the molten globule became.},
  Author                   = {O. B. Ptitsyn},
  Journal                  = {Trends Biochem Sci},
  Year                     = {1995},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {376--379},
  Volume                   = {20},

  Institution              = {Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow.},
  Keywords                 = {Animals; Cattle; Humans; Kinetics; Physical Phenomena; Physics; Protein Conformation; Protein Folding; Proteins, chemistry},
  Owner                    = {ranjan},
  Pii                      = {S0968-0004(00)89081-7},
  Pmid                     = {7482708},
  Timestamp                = {2010.05.02}
}

@Article{Ptitsyn1995d,
  Title                    = {Structures of folding intermediates.},
  Author                   = {O. B. Ptitsyn},
  Journal                  = {Curr Opin Struct Biol},
  Year                     = {1995},

  Month                    = {Feb},
  Number                   = {1},
  Pages                    = {74--78},
  Volume                   = {5},

  Abstract                 = {The past year has yielded important results in the study of protein-folding intermediates. It has been shown that the equilibrium molten globule has a native-like tertiary fold and is separated from the unfolded state by a first-order phase transition. New equilibrium intermediates have been revealed and substantial progress has been made in the understanding of two main barriers in protein folding.},
  Institution              = {Institute of Protein Research, Puschino, Russia.},
  Keywords                 = {Protein Folding},
  Owner                    = {ranjan},
  Pmid                     = {7773749},
  Timestamp                = {2010.05.02}
}

@Article{Ptitsyn1995e,
  Title                    = {Molten globule and protein folding.},
  Author                   = {O. B. Ptitsyn},
  Journal                  = {Adv Protein Chem},
  Year                     = {1995},
  Pages                    = {83--229},
  Volume                   = {47},

  Institution              = {Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.},
  Keywords                 = {Evolution; Guanidine; Guanidines, pharmacology; Kinetics; Membrane Proteins, chemistry/metabolism; Models, Molecular; Mutation; Protein Conformation; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins, chemistry/genetics/metabolism; Urea, pharmacology},
  Owner                    = {ranjan},
  Pmid                     = {8561052},
  Timestamp                = {2010.05.02}
}

@Article{Radford2000,
  Title                    = {Protein folding: progress made and promises ahead},
  Author                   = {Radford, Sheena E},
  Journal                  = {Trends in biochemical sciences},
  Year                     = {2000},
  Number                   = {12},
  Pages                    = {611--618},
  Volume                   = {25},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.08.15}
}

@Article{Radivojac2007,
  Title                    = {Intrinsic disorder and functional proteomics.},
  Author                   = {Radivojac, Predrag and Iakoucheva, Lilia M. and Oldfield, Christopher J. and Obradovic, Zoran and Uversky, Vladimir N. and Dunker, A Keith},
  Journal                  = {Biophys J},
  Year                     = {2007},

  Month                    = {Mar},
  Number                   = {5},
  Pages                    = {1439--1456},
  Volume                   = {92},

  Abstract                 = {The recent advances in the prediction of intrinsically disordered proteins and the use of protein disorder prediction in the fields of molecular biology and bioinformatics are reviewed here, especially with regard to protein function. First, a close look is taken at intrinsically disordered proteins and then at the methods used for their experimental characterization. Next, the major statistical properties of disordered regions are summarized, and prediction models developed thus far are described, including their numerous applications in functional proteomics. The future of the prediction of protein disorder and the future uses of such predictions in functional proteomics comprise the last section of this article.},
  Doi                      = {10.1529/biophysj.106.094045},
  Institution              = {School of Informatics, Indiana University, Bloomington, Indiana, USA.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Animals; Computational Biology; Data Interpretation, Statistical; Databases, Protein; Humans; Molecular Sequence Data; Protein Conformation; Protein Folding; Protein Processing, Post-Translational; Proteins, chemistry/physiology; Proteomics, methods},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0006-3495(07)70955-4},
  Pmid                     = {17158572},
  Timestamp                = {2013.12.08}
}

@Article{Radivojac2004,
  Title                    = {Protein flexibility and intrinsic disorder.},
  Author                   = {Radivojac, Predrag and Obradovic, Zoran and Smith, David K. and Zhu, Guang and Vucetic, Slobodan and Brown, Celeste J. and Lawson, J David and Dunker, A Keith},
  Journal                  = {Protein Sci},
  Year                     = {2004},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {71--80},
  Volume                   = {13},

  Abstract                 = {Comparisons were made among four categories of protein flexibility: (1) low-B-factor ordered regions, (2) high-B-factor ordered regions, (3) short disordered regions, and (4) long disordered regions. Amino acid compositions of the four categories were found to be significantly different from each other, with high-B-factor ordered and short disordered regions being the most similar pair. The high-B-factor (flexible) ordered regions are characterized by a higher average flexibility index, higher average hydrophilicity, higher average absolute net charge, and higher total charge than disordered regions. The low-B-factor regions are significantly enriched in hydrophobic residues and depleted in the total number of charged residues compared to the other three categories. We examined the predictability of the high-B-factor regions and developed a predictor that discriminates between regions of low and high B-factors. This predictor achieved an accuracy of 70\% and a correlation of 0.
43 with experimental data, outperforming the 64\% accuracy and 0.32 correlation of predictors based solely on flexibility indices. To further clarify the differences between short disordered regions and ordered regions, a predictor of short disordered regions was developed. Its relatively high accuracy of 81\% indicates considerable differences between ordered and disordered regions. The distinctive amino acid biases of high-B-factor ordered regions, short disordered regions, and long disordered regions indicate that the sequence determinants for these flexibility categories differ from one another, whereas the significantly-greater-than-chance predictability of these categories from sequence suggest that flexible ordered regions, short disorder, and long disorder are, to a significant degree, encoded at the primary structure level.},
  Doi                      = {10.1110/ps.03128904},
  Institution              = {Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA.},
  Keywords                 = {Amino Acid Sequence; Amino Acids, chemistry; Confidence Intervals; Databases, Factual; Evolution, Molecular; Hydrophobic and Hydrophilic Interactions; Logistic Models; Predictive Value of Tests; Protein Conformation; Protein Folding; Protein Structure, Secondary; Proteins, chemistry/genetics; Reproducibility of Results; Sensitivity and Specificity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {14691223},
  Timestamp                = {2013.12.08}
}

@Article{Ragan2009,
  Title                    = {The network of life: genome beginnings and evolution. Introduction.},
  Author                   = {Ragan, Mark A. and McInerney, James O. and Lake, James A.},
  Journal                  = {Philos Trans R Soc Lond B Biol Sci},
  Year                     = {2009},

  Month                    = {Aug},
  Number                   = {1527},
  Pages                    = {2169--2175},
  Volume                   = {364},

  Institution              = {Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, Australia. m.ragan@imb.uq.edu.au},
  Keywords                 = {Ecosystem; Evolution, Molecular; Gene Transfer, Horizontal, genetics; Genetic Variation; Genome, genetics; Phylogeny},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {364/1527/2169},
  Pmid                     = {19571237},
  Timestamp                = {2012.07.09}
}

@Article{Ramachandran1955,
  Title                    = {Structure of collagen},
  Author                   = {Ramachandran, GN and Kartha, Gopinath},
  Journal                  = {Nature},
  Year                     = {1955},
  Pages                    = {593--595},
  Volume                   = {176}
}

@Article{Ramachandran1954,
  Title                    = {Structure of collagen},
  Author                   = {Ramachandran, GN and Kartha, Gopinath},
  Journal                  = {Nature},
  Year                     = {1954},
  Pages                    = {269--270},
  Volume                   = {174},

  Publisher                = {Nature Publishing Group}
}

@Article{Ramachandran1963,
  Title                    = {Stereochemistry of polypeptide chain configurations},
  Author                   = {Ramachandran, GN and Ramakrishnan, CT and Sasisekharan, V},
  Journal                  = {Journal of molecular biology},
  Year                     = {1963},
  Number                   = {1},
  Pages                    = {95--99},
  Volume                   = {7},

  Owner                    = {ranjan},
  Publisher                = {Academic Press},
  Timestamp                = {2015.03.04}
}

@PhdThesis{Randall1994,
  Title                    = {Counting in lattices: combinatorial problems from statistical mechanics},
  Author                   = {Randall, Dana Jill},
  School                   = {Citeseer},
  Year                     = {1994},

  Owner                    = {ranjan},
  Timestamp                = {2013.07.06}
}

@Article{Rao2010,
  Title                    = {Protein dynamics investigated by inherent structure analysis},
  Author                   = {Rao, Francesco and Karplus, Martin},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2010},
  Number                   = {20},
  Pages                    = {9152--9157},
  Volume                   = {107},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2015.06.29}
}

@Article{Rapaport2004,
  Title                    = {Self-assembly of polyhedral shells: A molecular dynamics study},
  Author                   = {Rapaport, D. C.},
  Journal                  = PRE,
  Year                     = {2004},
  Number                   = {5},
  Pages                    = {1539--1555},
  Volume                   = {70},

  File                     = {Rapaport2004.pdf:pdfs/Rapaport2004.pdf:PDF}
}

@Article{Rasmussen2000,
  Title                    = {Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit.},
  Author                   = {Rasmussen, B.},
  Journal                  = {Nature},
  Year                     = {2000},

  Month                    = {Jun},
  Number                   = {6787},
  Pages                    = {676--679},
  Volume                   = {405},

  Abstract                 = {The record of Archaean microfossils is sparse. Of the few bona fide fossil assemblages, most are from shallow-water settings, and they are typically associated with laminated, stromatolitic sedimentary rocks. Microfossils from deep-sea hydrothermal systems have not been reported in Precambrian rocks (> 544 million years old), although thermophilic microbes are ubiquitous in modern sea-floor hydrothermal settings, and apparently have the most ancient lineages. Here, I report the discovery of pyritic filaments, the probable fossil remains of thread-like microorganisms, in a 3,235-million-year-old deep-sea volcanogenic massive sulphide deposit from the Pilbara Craton of Australia. From their mode of occurrence, the micro-organisms were probably thermophilic chemotropic prokaryotes, which inhabited sub-sea-floor hydrothermal environments. They represent the first fossil evidence for microbial life in a Precambrian submarine thermal spring system, and extend the known range of 
submarine hydrothermal biota by more than 2,700 million years. Such environments may have hosted the first living systems on Earth, consistent with proposals for a thermophilic origin of life.},
  Institution              = {Department of Geology and Geophysics, University of Western Australia, Nedlands, Australia. brasmuss@geol.uwa.edu.au},
  Keywords                 = {Archaea; Australia; Biogenesis; Biological Evolution; Fossils; Sulfides; Water Microbiology},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {10864322},
  Timestamp                = {2012.04.06}
}

@Article{Receveur-Brechot2006,
  Title                    = {Assessing protein disorder and induced folding.},
  Author                   = {Receveur-Bréchot, Véronique and Bourhis, Jean-Marie and Uversky, Vladimir N. and Canard, Bruno and Longhi, Sonia},
  Journal                  = {Proteins},
  Year                     = {2006},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {24--45},
  Volume                   = {62},

  Abstract                 = {Intrinsically disordered proteins (IDPs) defy the structure-function paradigm as they fulfill essential biological functions while lacking well-defined secondary and tertiary structures. Conformational and spectroscopic analyses showed that IDPs do not constitute a uniform family, and can be divided into subfamilies as a function of their residual structure content. Residual intramolecular interactions are thought to facilitate binding to a partner and then induced folding. Comprehensive information about experimental approaches to investigate structural disorder and induced folding is still scarce. We herein provide hints to readily recognize features typical of intrinsic disorder and review the principal techniques to assess structural disorder and induced folding. We describe their theoretical principles and discuss their respective advantages and limitations. Finally, we point out the necessity of using different approaches and show how information can be broadened by the 
use of multiples techniques.},
  Doi                      = {10.1002/prot.20750},
  Institution              = {Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Universités Aix-Marseille I et II, Campus de Luminy, Marseille Cedex 09, France.},
  Keywords                 = {Amino Acid Sequence; Circular Dichroism; Protein Conformation; Protein Folding; Protein Structure, Secondary; Proteins, chemistry/metabolism; X-Ray Diffraction},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {16287116},
  Timestamp                = {2013.12.12}
}

@Article{Rechnitzer2002,
  Title                    = {Canonical Monte Carlo determination of the connective constant of self-avoiding walks},
  Author                   = {Rechnitzer, A and van Rensburg, EJ Janse},
  Journal                  = {Journal of Physics A: Mathematical and General},
  Year                     = {2002},
  Number                   = {42},
  Pages                    = {L605},
  Volume                   = {35},

  Owner                    = {ranjan},
  Publisher                = {IOP Publishing},
  Timestamp                = {2013.07.06}
}

@InBook{Reddy2005,
  Title                    = {Virus Structure and Assembly (Advances in Virus Research)},
  Author                   = {Reddy,V.S. and Johnson,J.E.},
  Chapter                  = {Structure-Derived Insights into Virus Assembly.},
  Pages                    = {45--468},
  Publisher                = {Elserver Academic Press},
  Year                     = {2005},

  Address                  = {San Diego, CA, USA}
}

@Article{Renfrew2014,
  Title                    = {A Rotamer Library to Enable Modeling and Design of Peptoid Foldamers},
  Author                   = {Renfrew, P Douglas and Craven, Timothy W and Butterfoss, Glenn L and Kirshenbaum, Kent and Bonneau, Richard},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {2014},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2014.08.25}
}

@Article{Rensburg2009,
  Title                    = {Generalized atmospheric sampling of self-avoiding walks},
  Author                   = {van Rensburg, EJ Janse and Rechnitzer, A},
  Journal                  = {Journal of Physics A: Mathematical and Theoretical},
  Year                     = {2009},
  Number                   = {33},
  Pages                    = {335001},
  Volume                   = {42},

  Owner                    = {ranjan},
  Publisher                = {IOP Publishing},
  Timestamp                = {2014.08.31}
}

@Article{Rice2004,
  Title                    = {The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life},
  Author                   = {Rice,G. and Tang,L. and Stedman,K. and Roberto,F. and Spuhler,J. and Gillitzer,E. and Johnson,J.E. and Douglas,T. and Young,M.},
  Journal                  = {Trends Biotechnol.},
  Year                     = {2004},
  Number                   = {20},
  Pages                    = {7716--7720},
  Volume                   = {101}
}

@Article{Rich1955,
  Title                    = {The Structure of Collagen},
  Author                   = {Rich, Alexander and Crick, FHC},
  Journal                  = {Nature},
  Year                     = {1955},
  Pages                    = {915--916},
  Volume                   = {176}
}

@Article{Riddle1997,
  Title                    = {Functional rapidly folding proteins from simplified amino acid sequences.},
  Author                   = {D. S. Riddle and J. V. Santiago and S. T. Bray-Hall and N. Doshi and V. P. Grantcharova and Q. Yi and D. Baker},
  Journal                  = {Nat Struct Biol},
  Year                     = {1997},

  Month                    = {Oct},
  Number                   = {10},
  Pages                    = {805--809},
  Volume                   = {4},

  Abstract                 = {Early protein synthesis is thought to have involved a reduced amino acid alphabet. What is the minimum number of amino acids that would have been needed to encode complex protein folds similar to those found in nature today? Here we show that a small beta-sheet protein, the SH3 domain, can be largely encoded by a five letter amino acid alphabet but not by a three letter alphabet. Furthermore, despite the dramatic changes in sequence, the folding rates of the reduced alphabet proteins are very close to that of the naturally occurring SH3 domain. This finding suggests that despite the vast size of the search space, the rapid folding of biological sequences to their native states is not the result of extensive evolutionary optimization. Instead, the results support the idea that the interactions which stabilize the native state induce a funnel shape to the free energy landscape sufficient to guide the folding polypeptide chain to the proper structure.},
  File                     = {Riddle1997.pdf:pdfs/Riddle1997.pdf:PDF},
  Institution              = {Department of Biochemistry, University of Washington, Seattle 98195, USA.},
  Keywords                 = {Amino Acid Sequence; Calorimetry; Cloning, Molecular; Conserved Sequence; Genes, src; Guanidine; Kinetics; Models, Molecular; Molecular Sequence Data; Peptide Library; Protein Biosynthesis; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Proteins, chemistry; Sequence Alignment; Thermodynamics; src Homology Domains},
  Owner                    = {ranjan},
  Pmid                     = {9334745},
  Timestamp                = {2009.10.03}
}

@Article{Robertson2014,
  Title                    = {Assembly and molecular order of two-dimensional peptoid nanosheets through the oil--water interface},
  Author                   = {Robertson, Ellen J and Oliver, Gloria K and Qian, Menglu and Proulx, Caroline and Zuckermann, Ronald N and Richmond, Geraldine L},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2014},
  Number                   = {37},
  Pages                    = {13284--13289},
  Volume                   = {111},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2015.04.14}
}

@Article{Roland2007,
  Title                    = {Divergent evolution of a structural proteome: phenomenological models.},
  Author                   = {C. Brian Roland and Eugene I Shakhnovich},
  Journal                  = {Biophys J},
  Year                     = {2007},

  Month                    = {Feb},
  Number                   = {3},
  Pages                    = {701--716},
  Volume                   = {92},

  Abstract                 = {We develop models of the divergent evolution of genomes; the elementary object of sequence dynamics is the protein structural domain. To identify patterns of organization that reflect mechanisms of evolution, we consider the individual genomes of many procaryote species, studying the arrangement of protein structural domains in the space of all polypeptide structures. We view the network of structural similarities as a graph, called the organismal Protein Domain Universe Graph (oPDUG); vertices represent types of structural domains and edges represent strong structural similarity. As observed before, each oPDUG is a highly nonrandom graph, as evidenced in the vertex degree distribution, which resembles a Pareto law (which has a power-law asymptotic). To explain this and other peculiar properties of the oPDUGs, we construct an evolving-graph model for the long-timescale evolutionary dynamics of oPDUGs, containing only divergent mechanisms of domain discovery. The model generates 
degree distributions (resembling Pareto laws) and clustering-coefficient distributions that are characteristic of the oPDUGs. In the infinite-graph limit, we analytically compute the exponent for specific biological parameters, as well as the complete phase diagram of the model, finding two distinct regimes of domain innovation dynamics. Thus, divergent evolutionary dynamics quantitatively explains the nonrandom organization of oPDUGs.},
  Institution              = {Chemical Physics Program, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.},
  Keywords                 = {Bacterial Proteins, genetics; Chromosome Mapping, methods; Computer Simulation; DNA Mutational Analysis, methods; Evolution, Molecular; Genetic Variation, genetics; Models, Genetic; Models, Statistical; Protein Structure, Tertiary, genetics; Proteome, genetics},
  Owner                    = {ranjan},
  Pii                      = {S0006-3495(07)70882-2},
  Pmid                     = {17071665},
  Timestamp                = {2009.12.05}
}

@Article{Romero1997,
  Title                    = {Identifying disordered regions in proteins from amino acid sequences},
  Author                   = {Romero, P. and Obradovic, Z. and Kissinger, C. R. and Villafranca, J. E. and and Dunker, A. K.},
  Journal                  = {IEEE Int. Conf. Neural Netw.},
  Year                     = {1997},
  Pages                    = {90--95},
  Volume                   = {1},

  Owner                    = {ranjan},
  Timestamp                = {2013.12.08}
}

@Article{Romero2001,
  Title                    = {Sequence complexity of disordered protein.},
  Author                   = {Romero, P. and Obradovic, Z. and Li, X. and Garner, E. C. and Brown, C. J. and Dunker, A. K.},
  Journal                  = {Proteins},
  Year                     = {2001},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {38--48},
  Volume                   = {42},

  Abstract                 = {Intrinsic disorder refers to segments or to whole proteins that fail to self-fold into fixed 3D structure, with such disorder sometimes existing in the native state. Here we report data on the relationships among intrinsic disorder, sequence complexity as measured by Shannon's entropy, and amino acid composition. Intrinsic disorder identified in protein crystal structures, and by nuclear magnetic resonance, circular dichroism, and prediction from amino acid sequence, all exhibit similar complexity distributions that are shifted to lower values compared to, but significantly overlapping with, the distribution for ordered proteins. Compared to sequences from ordered proteins, these variously characterized intrinsically disordered segments and proteins, and also a collection of low-complexity sequences, typically have obviously higher levels of protein-specific subsets of the following amino acids: R, K, E, P, and S, and lower levels of subsets of the following: C, W, Y, I, and V. 
The Swiss Protein database of sequences exhibits significantly higher amounts of both low-complexity and predicted-to-be-disordered segments as compared to a non-redundant set of sequences from the Protein Data Bank, providing additional data that nature is richer in disordered and low-complexity segments compared to the commonness of these features in the set of structurally characterized proteins.},
  Institution              = {School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington 99164-4660, USA. promero@ai.sri.com},
  Keywords                 = {Artificial Intelligence; Base Sequence; Databases, Factual; Models, Molecular; Protein Denaturation; Protein Folding; Protein Structure, Tertiary; Proteins, chemistry; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {3.0.CO;2-3},
  Pmid                     = {11093259},
  Timestamp                = {2013.12.08}
}

@Article{Roos2007,
  Title                    = {Modelling evolution on design-by-contract predicts an origin of life through an abiotic double-stranded RNA world.},
  Author                   = {Albert D G de Roos},
  Journal                  = {Biol Direct},
  Year                     = {2007},
  Pages                    = {12},
  Volume                   = {2},

  Abstract                 = {BACKGROUND: It is generally believed that life first evolved from single-stranded RNA (ssRNA) that both stored genetic information and catalyzed the reactions required for self-replication. PRESENTATION OF THE HYPOTHESIS: By modeling early genome evolution on the engineering paradigm design-by-contract, an alternative scenario is presented in which life started with the appearance of double-stranded RNA (dsRNA) as an informational storage molecule while catalytic single-stranded RNA was derived from this dsRNA template later in evolution. TESTING THE HYPOTHESIS: It was investigated whether this scenario could be implemented mechanistically by starting with abiotic processes. Double-stranded RNA could be formed abiotically by hybridization of oligoribonucleotides that are subsequently non-enzymatically ligated into a double-stranded chain. Thermal cycling driven by the diurnal temperature cycles could then replicate this dsRNA when strands of dsRNA separate and later rehybridize 
and ligate to reform dsRNA. A temperature-dependent partial replication of specific regions of dsRNA could produce the first template-based generation of catalytic ssRNA, similar to the developmental gene transcription process. Replacement of these abiotic processes by enzymatic processes would guarantee functional continuity. Further transition from a dsRNA to a dsDNA world could be based on minor mutations in template and substrate recognition sites of an RNA polymerase and would leave all existing processes intact. IMPLICATIONS OF THE HYPOTHESIS: Modeling evolution on a design pattern, the 'dsRNA first' hypothesis can provide an alternative mechanistic evolutionary scenario for the origin of our genome that preserves functional continuity. REVIEWERS: This article was reviewed by Anthony Poole, Eugene Koonin and Eugene Shakhnovich.},
  Institution              = {Syncyte BioIntelligence, PO Box 600, 1000 AP Amsterdam, The Netherlands. albert.de.roos@syncyte.com},
  Owner                    = {ranjan},
  Pii                      = {1745-6150-2-12},
  Pmid                     = {17466073},
  Timestamp                = {2009.12.05}
}

@Article{Rosales2010,
  Title                    = {Control of crystallization and melting behavior in sequence specific polypeptoids},
  Author                   = {Rosales, Adrianne M and Murnen, Hannah K and Zuckermann, Ronald N and Segalman, Rachel A},
  Journal                  = {Macromolecules},
  Year                     = {2010},
  Number                   = {13},
  Pages                    = {5627--5636},
  Volume                   = {43},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2015.06.09}
}

@Book{Rosen2012,
  Title                    = {Surfactants and interfacial phenomena},
  Author                   = {Rosen, Milton J and Kunjappu, Joy T},
  Publisher                = {John Wiley \& Sons},
  Year                     = {2012},

  Owner                    = {ranjan},
  Timestamp                = {2015.01.18}
}

@Article{Rossmann1989,
  Title                    = {Icosahedral RNA virus structure},
  Author                   = {Rossmann, M. G. and Johnson, J. E.},
  Journal                  = ARB,
  Year                     = {1989},
  Pages                    = {533--573},
  Volume                   = {58}
}

@Article{Rux2008,
  Title                    = {Spherical viruses.},
  Author                   = {Rux, J.J. and Burnett, R.M.},
  Journal                  = {Curr Opin Struct Biol.},
  Year                     = {2008},
  Number                   = {2},
  Pages                    = {142--149},
  Volume                   = {8}
}

@Book{Sadoc1999,
  Title                    = {Geometrical frustration},
  Author                   = {Sadoc, J. F. and Mosseri, R.},
  Publisher                = {Cambridge University Press},
  Year                     = {1999},

  Address                  = {Cambridge, UK}
}

@Article{Saghatelian2001,
  Title                    = {A chiroselective peptide replicator.},
  Author                   = {A. Saghatelian and Y. Yokobayashi and K. Soltani and M. R. Ghadiri},
  Journal                  = {Nature},
  Year                     = {2001},

  Month                    = {Feb},
  Number                   = {6822},
  Pages                    = {797--801},
  Volume                   = {409},

  Abstract                 = {The origin of homochirality in living systems is often attributed to the generation of enantiomeric differences in a pool of chiral prebiotic molecules, but none of the possible physiochemical processes considered can produce the significant imbalance required if homochiral biopolymers are to result from simple coupling of suitable precursor molecules. This implies a central role either for additional processes that can selectively amplify an initially minute enantiomeric difference in the starting material, or for a nonenzymatic process by which biopolymers undergo chiroselective molecular replication. Given that molecular self-replication and the capacity for selection are necessary conditions for the emergence of life, chiroselective replication of biopolymers seems a particularly attractive process for explaining homochirality in nature. Here we report that a 32-residue peptide replicator, designed according to our earlier principles, is capable of efficiently amplifying 
homochiral products from a racemic mixture of peptide fragments through a chiroselective autocatalytic cycle. The chiroselective amplification process discriminates between structures possessing even single stereochemical mutations within otherwise homochiral sequences. Moreover, the system exhibits a dynamic stereochemical 'editing' function; in contrast to the previously observed error correction, it makes use of heterochiral sequences that arise through uncatalysed background reactions to catalyse the production of the homochiral product. These results support the idea that self-replicating polypeptides could have played a key role in the origin of homochirality on Earth.},
  Institution              = {Scripps Res Inst, La Jolla, CA},
  Keywords                 = {Amino Acid Sequence; Catalysis; Evolution, Chemical; Molecular Sequence Data; Mutation; Peptide Biosynthesis; Peptide Fragments, chemistry; Peptides, chemistry/genetics; Protein Conformation; Stereoisomerism; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {11236988},
  Timestamp                = {2011.08.12}
}

@Article{Sali1994a,
  Title                    = {Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.},
  Author                   = {A. Sali and E. Shakhnovich and M. Karplus},
  Journal                  = {J Mol Biol},
  Year                     = {1994},

  Month                    = {Feb},
  Number                   = {5},
  Pages                    = {1614--1636},
  Volume                   = {235},

  Abstract                 = {A three-dimensional lattice model of a protein is used to investigate the properties required for its folding to the native state. The polypeptide chain is represented as a 27 bead heteropolymer whose lowest energy (native) state can be determined by an exhaustive enumeration of all fully compact conformations. A total of 200 sequences with random interactions are generated and subjected to Monte Carlo simulations to determine which chains find the ground state in a short time; i.e. which sequences overcome the folding problem referred to as the Levinthal paradox. Comparison of the folding and non-folding sequences is used to identify the features that are required for fast folding to the global energy minimum. It is shown that successful folding does not require certain attributes that have been previously proposed as necessary for folding; these include a high number of short versus long-range contacts in the native state, a high content of the secondary structure in the 
native state, a strong correlation between the native contact map and the interaction parameters, and the existence of a high number of low energy states with near-native conformation. Instead, the essential difference between the folding and the non-folding sequences is the nature of the energy spectrum. The necessary and sufficient condition for a sequence to fold rapidly in the present model is that the native state is a pronounced energy minimum. As a consequence, the thermodynamic stability of the native state of a folding sequence has a sigmoidal dependence on temperature. This permits such a sequence to satisfy both the thermodynamic and the kinetic requirements for folding; i.e. the native state predominates thermodynamically at temperatures that are high enough for folding to be kinetically possible. The applicability of the present results to real proteins is discussed.},
  File                     = {Sali1994a.pdf:pdfs/Sali1994a.pdf:PDF},
  Institution              = {Department of Chemistry, Harvard University, Cambridge, MA 02138.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Kinetics; Mathematics; Models, Theoretical; Monte Carlo Method; Protein Conformation; Protein Folding; Protein Structure, Secondary; Proteins, chemistry/metabolism; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(84)71110-7},
  Pmid                     = {8107095},
  Timestamp                = {2010.01.19}
}

@Article{Sandelin2004,
  Title                    = {On hydrophobicity and conformational specificity in proteins.},
  Author                   = {Erik Sandelin},
  Journal                  = {Biophys J},
  Year                     = {2004},

  Month                    = {Jan},
  Number                   = {1 Pt 1},
  Pages                    = {23--30},
  Volume                   = {86},

  Abstract                 = {In this study we examine the distribution of hydrophobic residues in a nonredundant set of monomeric globular single-domain proteins. We find that the total fraction of hydrophobic residues is roughly constant and has no discernible dependence on protein size. This results in a decrease of the hydrophobicity of the core as the size of proteins increases. Using a normalized measure, and by comparing with sets of randomly reshuffled sequences, we show that this change in the composition of the core is statistically significant and robust with respect to which amino acids are considered hydrophobic and to how buried residues are defined. Comparison with model sequences optimized for stability, while still required to retain their native state as a unique minimum energy conformation, suggests that the size-independence of the total fraction of hydrophobic residues could be a result of requiring proteins to be conformationally specific.},
  Institution              = {Stockholm Bioinformatics Center, AlbaNova, Stockholms Universitet, Stockholm, Sweden. erik@sbc.su.se},
  Keywords                 = {Amino Acid Sequence; Binding Sites; Computer Simulation; Hydrophobicity; Models, Chemical; Molecular Sequence Data; Protein Binding; Protein Conformation; Proteins, chemistry; Sequence Analysis, Protein, methods; Structure-Activity Relationship; Water, chemistry},
  Owner                    = {ranjan},
  Pii                      = {S0006-3495(04)74080-1},
  Pmid                     = {14695246},
  Timestamp                = {2010.09.22}
}

@Article{Sangita2004,
  Title                    = {T=1 capsid structures of Sesbania mosaic virus coat protein mutants: determinants of T=3 and T=1 capsid assembly.},
  Author                   = {Sangita, V. and Lokesh, G. L. and Satheshkumar, P. S. and Vijay, C. S. and Saravanan, V. and Savithri, H. S. and Murthy, M. R.},
  Journal                  = JMB,
  Year                     = {2004},
  Number                   = {3},
  Pages                    = {987--999},
  Volume                   = {342},

  File                     = {Sangita2004.pdf:pdfs/Sangita2004.pdf:PDF}
}

@Article{Sangita2005,
  Title                    = {Structure of a mutant T=1 capsid of Sesbania mosaic virus: role of water molecules in capsid architecture and integrity.},
  Author                   = {Sangita, V. and Satheshkumar, P. S. and Savithri, H. S. and Murthy, M. R.},
  Journal                  = {Acta Crystallogr D Biol Crystallogr.},
  Year                     = {2005},
  Pages                    = {1406--1412},
  Volume                   = {61}
}

@Article{Sanii2014,
  Title                    = {Structure-Determining Step in the Hierarchical Assembly of Peptoid Nanosheets},
  Author                   = {Sanii, Babak and Haxton, Thomas K and Olivier, Gloria K and Cho, Andrew and Barton, Bastian and Proulx, Caroline and Whitelam, Stephen and Zuckermann, Ronald N},
  Journal                  = {ACS nano},
  Year                     = {2014},
  Number                   = {11},
  Pages                    = {11674--11684},
  Volume                   = {8},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2015.01.17}
}

@Article{Sanii2011,
  Title                    = {Shaken, not stirred: collapsing a peptoid monolayer to produce free-floating, stable nanosheets.},
  Author                   = {Sanii, Babak and Kudirka, Romas and Cho, Andrew and Venkateswaran, Neeraja and Olivier, Gloria K. and Olson, Alexander M. and Tran, Helen and Harada, R Marika and Tan, Li and Zuckermann, Ronald N.},
  Journal                  = {J Am Chem Soc},
  Year                     = {2011},

  Month                    = {Dec},
  Number                   = {51},
  Pages                    = {20808--20815},
  Volume                   = {133},

  Abstract                 = {Two-dimensional nanomaterials play a critical role in biology (e.g., lipid bilayers) and electronics (e.g., graphene) but are difficult to directly synthesize with a high level of precision. Peptoid nanosheet bilayers are a versatile synthetic platform for constructing multifunctional, precisely ordered two-dimensional nanostructures. Here we show that nanosheet formation occurs through an unusual monolayer intermediate at the air-water interface. Lateral compression of a self-assembled peptoid monolayer beyond a critical collapse pressure results in the irreversible production of nanosheets. An unusual thermodynamic cycle is employed on a preparative scale, where mechanical energy is used to buckle an intermediate monolayer into a more stable nanosheet. Detailed physical studies of the monolayer-compression mechanism revealed a simple preparative technique to produce nanosheets in 95\% overall yield by cyclical monolayer compressions in a rotating closed vial. Compression of 
monolayers into stable, free-floating products may be a general and preparative approach to access 2D nanomaterials.},
  Doi                      = {10.1021/ja206199d},
  Institution              = {The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.},
  Keywords                 = {Air; Models, Molecular; Nanostructures, chemistry/ultrastructure; Nanotechnology, methods; Peptoids, chemistry; Thermodynamics; Water, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {21939206},
  Timestamp                = {2014.04.26}
}

@Article{Santner2012,
  Title                    = {Sweeping away protein aggregation with entropic bristles: intrinsically disordered protein fusions enhance soluble expression.},
  Author                   = {Santner, Aaron A. and Croy, Carrie H. and Vasanwala, Farha H. and Uversky, Vladimir N. and Van, Ya-Yue J. and Dunker, A Keith},
  Journal                  = {Biochemistry},
  Year                     = {2012},

  Month                    = {Sep},
  Number                   = {37},
  Pages                    = {7250--7262},
  Volume                   = {51},

  Abstract                 = {Intrinsically disordered, highly charged protein sequences act as entropic bristles (EBs), which, when translationally fused to partner proteins, serve as effective solubilizers by creating both a large favorable surface area for water interactions and large excluded volumes around the partner. By extending away from the partner and sweeping out large molecules, EBs can allow the target protein to fold free from interference. Using both naturally occurring and artificial polypeptides, we demonstrate the successful implementation of intrinsically disordered fusions as protein solubilizers. The artificial fusions discussed herein have a low level of sequence complexity and a high net charge but are diversified by means of distinctive amino acid compositions and lengths. Using 6xHis fusions as controls, soluble protein expression enhancements from 65\% (EB60A) to 100\% (EB250) were observed for a 20-protein portfolio. Additionally, these EBs were able to more effectively solubilize 
targets compared to frequently used fusions such as maltose-binding protein, glutathione S-transferase, thioredoxin, and N utilization substance A. Finally, although these EBs possess very distinct physiochemical properties, they did not perturb the structure, conformational stability, or function of the green fluorescent protein or the glutathione S-transferase protein. This work thus illustrates the successful de novo design of intrinsically disordered fusions and presents a promising technology and complementary resource for researchers attempting to solubilize recalcitrant proteins.},
  Doi                      = {10.1021/bi300653m},
  Institution              = {Molecular Kinetics Inc., Indianapolis, Indiana 46268, United States.},
  Keywords                 = {Escherichia coli, genetics/metabolism; Protein Biosynthesis; Protein Folding; Recombinant Fusion Proteins, biosynthesis/chemistry/genetics; Solubility},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {22924672},
  Timestamp                = {2013.12.08}
}

@Article{Sanz2007,
  Title                    = {Evidence for out-of-equilibrium crystal nucleation in suspensions of oppositely charged colloids},
  Author                   = {Sanz, Eduardo and Valeriani, Chantal and Frenkel, Daan and Dijkstra, Marjolein},
  Journal                  = {Physical review letters},
  Year                     = {2007},
  Number                   = {5},
  Pages                    = {055501},
  Volume                   = {99},

  Owner                    = {ranjan},
  Publisher                = {APS},
  Timestamp                = {2015.04.20}
}

@Article{Saravanan2010,
  Title                    = {Sequence and structural analysis of two designed proteins with 88% identity adopting different folds.},
  Author                   = {Saravanan, K Mani and Balasubramanian, Harihar and Nallusamy, Saranya and Samuel, Selvaraj},
  Journal                  = {Protein Eng Des Sel},
  Year                     = {2010},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {911--918},
  Volume                   = {23},

  Abstract                 = {Protein folding is a natural phenomenon by which a sequence of amino acids folds into a unique functional three-dimensional structure. Although the sequence code that governs folding remains a mystery, one can identify key inter-residue contacts responsible for a given topology. In nature, there are many pairs of proteins of a given length that share little or no sequence identity. Similarly, there are many proteins that share a common topology but lack significant evidence of homology. In order to tackle this problem, protein engineering studies have been used to determine the minimal number of amino acid residues that codes for a particular fold. In recent years, the coupling of theoretical models and experiments in the study of protein folding has resulted in providing some fruitful clues. He et al. have designed two proteins with 88\% sequence identity, which adopt different folds and functions. In this work, we have systematically analysed these two proteins by performing 
pentapeptide search, secondary structure predictions, variation in inter-residue interactions and residue-residue pair preferences, surrounding hydrophobicity computations, conformational switching and energy computations. We conclude that the local secondary structural preference of the two designed proteins at the Nand C-terminal ends to adopt either coil or strand conformation may be a crucial factor in adopting the different folds. Early on during the process of folding, both proteins may choose different energetically favourable pathways to attain the different folds.},
  Institution              = {Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, TN 620024, India.},
  Keywords                 = {Amino Acid Sequence; Hydrophobic and Hydrophilic Interactions; Molecular Sequence Annotation; Molecular Sequence Data; Protein Engineering, methods; Protein Folding; Protein Stability; Protein Structure, Tertiary; Proteins, chemistry/genetics/metabolism; Sequence Alignment; Sequence Analysis, Protein; Sequence Homology, Amino Acid},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {gzq070},
  Pmid                     = {20952437},
  Timestamp                = {2013.06.13}
}

@Article{Sarkar2014,
  Title                    = {The genomic challenge to adaptationism},
  Author                   = {Sarkar, Sahotra},
  Journal                  = {The British Journal for the Philosophy of Science},
  Year                     = {2014},
  Pages                    = {axu002},

  Owner                    = {ranjan},
  Publisher                = {Br Soc Philosophy Sci},
  Timestamp                = {2015.06.24}
}

@Article{Sayers2009,
  Title                    = {Database resources of the National Center for Biotechnology Information.},
  Author                   = {Eric W Sayers and Tanya Barrett and Dennis A Benson and Stephen H Bryant and Kathi Canese and Vyacheslav Chetvernin and Deanna M Church and Michael DiCuccio and Ron Edgar and Scott Federhen and Michael Feolo and Lewis Y Geer and Wolfgang Helmberg and Yuri Kapustin and David Landsman and David J Lipman and Thomas L Madden and Donna R Maglott and Vadim Miller and Ilene Mizrachi and James Ostell and Kim D Pruitt and Gregory D Schuler and Edwin Sequeira and Stephen T Sherry and Martin Shumway and Karl Sirotkin and Alexandre Souvorov and Grigory Starchenko and Tatiana A Tatusova and Lukas Wagner and Eugene Yaschenko and Jian Ye},
  Journal                  = {Nucleic Acids Res},
  Year                     = {2009},

  Month                    = {Jan},
  Number                   = {Database issue},
  Pages                    = {D5--15},
  Volume                   = {37},

  Abstract                 = {In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture 
Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.},
  Institution              = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA. sayers@ncbi.nlm.nih.gov},
  Keywords                 = {Databases, Genetic; Gene Expression; Genes; Genomics; Genotype; National Library of Medicine (U.S.); Phenotype; Protein Structure, Tertiary; Proteomics; PubMed; Sequence Homology; Systems Integration; United States},
  Owner                    = {ranjan},
  Pii                      = {gkn741},
  Pmid                     = {18940862},
  Timestamp                = {2009.10.01}
}

@Article{Scalan1970,
  Title                    = {An improved measure of the odd-even predominance in the normal alkanes of sediment extracts and petroleum},
  Author                   = {Scalan, E.S and Smith, J.E},
  Journal                  = {Geochimica et Cosmochimica Acta},
  Year                     = {1970},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {611-620},
  Volume                   = {34},

  Doi                      = {10.1016/0016-7037(70)90019-0},
  Owner                    = {ranjan},
  Publisher                = {Elsevier },
  Timestamp                = {2014.01.17}
}

@Article{Scarlett2010,
  Title                    = {Computational analysis of binary segregation during colloidal crystallization with DNA-mediated interactions},
  Author                   = {Scarlett, Raynaldo T and Crocker, John C and Sinno, Talid},
  Journal                  = {The Journal of chemical physics},
  Year                     = {2010},
  Number                   = {23},
  Pages                    = {234705},
  Volume                   = {132},

  Owner                    = {ranjan},
  Publisher                = {AIP Publishing},
  Timestamp                = {2015.04.20}
}

@Article{Scarlett2011,
  Title                    = {A mechanistic view of binary colloidal superlattice formation using DNA-directed interactions},
  Author                   = {Scarlett, Raynaldo T and Ung, Marie T and Crocker, John C and Sinno, Talid},
  Journal                  = {Soft Matter},
  Year                     = {2011},
  Number                   = {5},
  Pages                    = {1912--1925},
  Volume                   = {7},

  Owner                    = {ranjan},
  Publisher                = {Royal Society of Chemistry},
  Timestamp                = {2015.04.20}
}

@Article{Schad2011,
  Title                    = {The relationship between proteome size, structural disorder and organism complexity.},
  Author                   = {Schad, Eva and Tompa, Peter and Hegyi, Hedi},
  Journal                  = {Genome Biol},
  Year                     = {2011},
  Number                   = {12},
  Pages                    = {R120},
  Volume                   = {12},

  Abstract                 = {Sequencing the genomes of the first few eukaryotes created the impression that gene number shows no correlation with organism complexity, often referred to as the G-value paradox. Several attempts have previously been made to resolve this paradox, citing multifunctionality of proteins, alternative splicing, microRNAs or non-coding DNA. As intrinsic protein disorder has been linked with complex responses to environmental stimuli and communication between cells, an additional possibility is that structural disorder may effectively increase the complexity of species.We revisited the G-value paradox by analyzing many new proteomes whose complexity measured with their number of distinct cell types is known. We found that complexity and proteome size measured by the total number of amino acids correlate significantly and have a power function relationship. We systematically analyzed numerous other features in relation to complexity in several organisms and tissues and found: the 
fraction of protein structural disorder increases significantly between prokaryotes and eukaryotes but does not further increase over the course of evolution; the number of predicted binding sites in disordered regions in a proteome increases with complexity; the fraction of protein disorder, predicted binding sites, alternative splicing and protein-protein interactions all increase with the complexity of human tissues.We conclude that complexity is a multi-parametric trait, determined by interaction potential, alternative splicing capacity, tissue-specific protein disorder and, above all, proteome size. The G-value paradox is only apparent when plants are grouped with metazoans, as they have a different relationship between complexity and proteome size.},
  Keywords                 = {Algorithms; Alternative Splicing; Amino Acids, genetics; Bacteria, genetics; Binding Sites; Biological Evolution; Computational Biology; Databases, Protein; Eukaryota, genetics; Genome Size; Humans; Plants, genetics; Protein Folding; Protein Interaction Maps; Proteome, genetics; Proteostasis Deficiencies, genetics},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {gb-2011-12-12-r120},
  Pmid                     = {22182830},
  Timestamp                = {2012.09.26}
}

@Article{Schatz2012,
  Title                    = {Computational thinking in the era of big data biology},
  Author                   = {Schatz, Michael C},
  Journal                  = {Genome biology},
  Year                     = {2012},
  Number                   = {11},
  Pages                    = {1},
  Volume                   = {13},

  Owner                    = {ranjan},
  Publisher                = {BioMed Central},
  Timestamp                = {2016.07.17}
}

@Article{Schenk1997,
  Title                    = {Molecular evolutionary analysis of the thiamine-diphosphate-dependent enzyme, transketolase.},
  Author                   = {G. Schenk and R. Layfield and J. M. Candy and R. G. Duggleby and P. F. Nixon},
  Journal                  = {J Mol Evol},
  Year                     = {1997},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {552--572},
  Volume                   = {44},

  Abstract                 = {Members of the transketolase group of thiamine-diphosphate-dependent enzymes from 17 different organisms including mammals, yeast, bacteria, and plants have been used for phylogenetic reconstruction. Alignment of the amino acid and DNA sequences for 21 transketolase enzymes and one putative transketolase reveals a number of highly conserved regions and invariant residues that are of predicted importance for enzyme activity, based on the crystal structure of yeast transketolase. One particular sequence of 36 residues has some similarities to the nucleotide-binding motif and we designate it as the transketolase motif. We report further evidence that the recP protein from Streptococcus pneumoniae might be a transketolase and we list a number of invariant residues which might be involved in substrate binding. Phylogenies derived from the nucleotide and the amino acid sequences by various methods show a conventional clustering for mammalian, plant, and gram-negative bacterial 
transketolases. The branching order of the gram-positive bacteria could not be inferred reliably. The formaldehyde transketolase (sometimes known as dihydroxyacetone synthase) of the yeast Hansenula polymorpha appears to be orthologous to the mammalian enzymes but paralogous to the other yeast transketolases. The occurrence of more than one transketolase gene in some organisms is consistent with several gene duplications. The high degree of similarity in functionally important residues and the fact that the same kinetic mechanism is applicable to all characterized transketolase enzymes is consistent with the proposition that they are all derived from one common ancestral gene. Transketolase appears to be an ancient enzyme that has evolved slowly and might serve as a model for a molecular clock, at least within the mammalian clade.},
  Institution              = {Department of Biochemistry, Centre for Protein Structure, Function and Engineering, The University of Queensland, St. Lucia, QLD 4072, Australia.},
  Keywords                 = {Amino Acid Sequence; Amino Acids, analysis; Animals; Bacteria, enzymology; Base Composition; Conserved Sequence, genetics; DNA, genetics; Evolution, Molecular; Genes, genetics; Humans; Mammals; Models, Molecular; Molecular Sequence Data; Phylogeny; Plants, enzymology; Protein Structure, Secondary; Sequence Alignment; Streptococcus pneumoniae, enzymology; Transketolase, chemistry/genetics; Yeasts, enzymology},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9115179},
  Timestamp                = {2011.09.15}
}

@Article{Schiemann2005,
  Title                    = {Exact sequence analysis for three-dimensional hydrophobic-polar lattice proteins.},
  Author                   = {Schiemann, Reinhard and Bachmann, Michael and Janke, Wolfhard},
  Journal                  = {J Chem Phys},
  Year                     = {2005},

  Month                    = {Mar},
  Number                   = {11},
  Pages                    = {114705},
  Volume                   = {122},

  Abstract                 = {We have exactly enumerated all sequences and conformations of hydrophobic-polar (HP) proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the HP model, where only two types of monomers are distinguished, we determined and statistically analyzed designing sequences, i.e., sequences that have a nondegenerate ground state. Furthermore we were interested in characteristic thermodynamic properties of HP proteins with designing sequences. In order to be able to perform these exact studies, we applied an efficient enumeration method based on contact sets.},
  Institution              = {Institut f\"{u}r Theoretische Physik, Universit\"{a}t Leipzig, Germany. Reinhard.Schiemann@itp.uni-leipzig.de},
  Keywords                 = {Amino Acid Sequence; Binding Sites; Computer Simulation; Models, Chemical; Models, Molecular; Models, Statistical; Molecular Sequence Data; Protein Binding; Protein Conformation; Proteins, chemistry; Sequence Analysis, Protein, methods; Structure-Activity Relationship},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {15836241},
  Timestamp                = {2012.05.09}
}

@Article{Schierup2000,
  Title                    = {Consequences of recombination on traditional phylogenetic analysis.},
  Author                   = {Schierup, M. H. and Hein, J.},
  Journal                  = {Genetics},
  Year                     = {2000},

  Month                    = {Oct},
  Number                   = {2},
  Pages                    = {879--891},
  Volume                   = {156},

  Abstract                 = {We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination. With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may not be immediately detectable in a data set. The phylogenies when recombination is 
present superficially resemble phylogenies for sequences from an exponentially growing population. However, exponential growth has a different effect on statistics such as Tajima's D. Furthermore, ignoring recombination leads to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets.},
  Institution              = {Department of Ecology and Genetics, University of Aarhus, DK-8000 Aarhus C., Denmark. mikkel.schierup@biology.au.dk},
  Keywords                 = {Artifacts; Computer Simulation; DNA, Mitochondrial, genetics; DNA, Viral, genetics; Models, Genetic; Models, Statistical; Phylogeny; Recombination, Genetic; Software},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {11014833},
  Timestamp                = {2012.07.09}
}

@Book{Schlick2002,
  Title                    = {Molecular Modeling and Simulation},
  Author                   = {Tamar Schlick},
  Publisher                = {Springer},
  Year                     = {2002},

  Owner                    = {ranjan},
  Timestamp                = {2012.07.14}
}

@Article{Schmidt2005,
  Title                    = {Statistical Approaches to the Evenodd Effect in Fission},
  Author                   = {K.H. Schmidt and A. V. Ignatyuk and F. Rejmund and A. Keli and M. V. Ricciardi},
  Journal                  = {AIP Conference Proceedings},
  Year                     = {2005},
  Pages                    = {239-246},
  Volume                   = {798},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Schnell2007,
  Title                    = {Is the intrinsic disorder of proteins the cause of the scale-free architecture of protein--protein interaction networks?},
  Author                   = {Schnell, Santiago and Fortunato, Santo and Roy, Sourav},
  Journal                  = {Proteomics},
  Year                     = {2007},
  Number                   = {6},
  Pages                    = {961--964},
  Volume                   = {7},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2013.12.06}
}

@Article{Schopf2007,
  Title                    = {Evidence of Archean life: Stromatolites and microfossils},
  Author                   = {J. William Schopf and Anatoliy B. Kudryavtsev and Andrew D. Czaja and Abhishek B. Tripathi},
  Journal                  = {Precambrian Research},
  Year                     = {2007},
  Pages                    = {141--155},
  Volume                   = {158},

  Owner                    = {ranjan},
  Timestamp                = {2012.04.06}
}

@Article{Schroder2007,
  Title                    = {Joint experimental and theoretical investigation of the propensity of peptoids as drug carriers},
  Author                   = {Tina Schr\"{o}der and Aina Quintilla and Julia Setzler and Esther Birtalan and Wolfgang Wenzel and Stefan Br\"{a}se},
  Journal                  = {WSEAS Transactions on Biology and Biomedicine},
  Year                     = {2007},
  Number                   = {10},
  Pages                    = {145-148},
  Volume                   = {4},

  Owner                    = {ranjan},
  Timestamp                = {2012.07.15}
}

@Article{Schreiber2011,
  Title                    = {Protein binding specificity versus promiscuity},
  Author                   = {Schreiber, Gideon and Keating, Amy E},
  Journal                  = {Current opinion in structural biology},
  Year                     = {2011},
  Number                   = {1},
  Pages                    = {50--61},
  Volume                   = {21},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.17}
}

@Article{Schug2010,
  Title                    = {From protein folding to protein function and biomolecular binding by energy landscape theory},
  Author                   = {Schug, Alexander and Onuchic, Jos{\'e} N},
  Journal                  = {Current opinion in pharmacology},
  Year                     = {2010},
  Number                   = {6},
  Pages                    = {709--714},
  Volume                   = {10},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2014.09.02}
}

@Article{Schultz1995,
  Title                    = {From molecular diversity to catalysis: lessons from the immune system.},
  Author                   = {P. G. Schultz and R. A. Lerner},
  Journal                  = {Science},
  Year                     = {1995},

  Month                    = {Sep},
  Number                   = {5232},
  Pages                    = {1835--1842},
  Volume                   = {269},

  Abstract                 = {By combining the enormous molecular diversity of the immune system with basic mechanistic principles of chemistry, one can produce catalytic antibodies that allow control of reactions in ways heretofore not possible. Mechanistic and structural studies of these antibodies are also providing insights into important aspects of enzymatic catalysis and the evolution of catalytic function. Moreover, the ability to rationally direct the immune response to generate selective catalysts for reactions ranging from pericyclic and redox reactions to cationic rearrangement reactions underscores the chemical potential of this and other large combinatorial libraries.},
  Institution              = {Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley 94720, USA.},
  Keywords                 = {Amino Acid Sequence; Antibodies, Catalytic, chemistry/metabolism; Antibody Diversity; Binding Sites; Catalysis; Crystallography, X-Ray; Haptens, immunology; Humans; Molecular Sequence Data; Selection (Genetics); Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {7569920},
  Timestamp                = {2009.12.05}
}

@Article{Schulz1990,
  Title                    = {Induced-fit movements in adenylate kinases},
  Author                   = {Schulz, Georg E and M{\"u}ller, Christoph W and Diederichs, Kay},
  Journal                  = {Journal of molecular biology},
  Year                     = {1990},
  Number                   = {4},
  Pages                    = {627--630},
  Volume                   = {213},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.17}
}

@Article{Schwartz2000,
  Title                    = {`Local Rules' Theory Applied to Polyomavirus Polymorphic Capsid Assemblies},
  Author                   = {Schwartz, R. S. and Garcea, R. L. and Berger, B.},
  Journal                  = {Virology},
  Year                     = {2000},
  Number                   = {2},
  Pages                    = {461--470},
  Volume                   = {268},

  File                     = {Schwartz2000.pdf:pdfs/Schwartz2000.pdf:PDF}
}

@Article{Sen2004,
  Title                    = {Predicting binding sites of hydrolase-inhibitor complexes by combining several methods.},
  Author                   = {Taner Z Sen and Andrzej Kloczkowski and Robert L Jernigan and Changhui Yan and Vasant Honavar and Kai-Ming Ho and Cai-Zhuang Wang and Yungok Ihm and Haibo Cao and Xun Gu and Drena Dobbs},
  Journal                  = {BMC Bioinformatics},
  Year                     = {2004},
  Pages                    = {205},
  Volume                   = {5},

  Abstract                 = {BACKGROUND: Protein-protein interactions play a critical role in protein function. Completion of many genomes is being followed rapidly by major efforts to identify interacting protein pairs experimentally in order to decipher the networks of interacting, coordinated-in-action proteins. Identification of protein-protein interaction sites and detection of specific amino acids that contribute to the specificity and the strength of protein interactions is an important problem with broad applications ranging from rational drug design to the analysis of metabolic and signal transduction networks. RESULTS: In order to increase the power of predictive methods for protein-protein interaction sites, we have developed a consensus methodology for combining four different methods. These approaches include: data mining using Support Vector Machines, threading through protein structures, prediction of conserved residues on the protein surface by analysis of phylogenetic trees, and the 
Conservatism of Conservatism method of Mirny and Shakhnovich. Results obtained on a dataset of hydrolase-inhibitor complexes demonstrate that the combination of all four methods yield improved predictions over the individual methods. CONCLUSIONS: We developed a consensus method for predicting protein-protein interface residues by combining sequence and structure-based methods. The success of our consensus approach suggests that similar methodologies can be developed to improve prediction accuracies for other bioinformatic problems.},
  Institution              = {L.H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA. taner@iastate.edu},
  Keywords                 = {Algorithms; Bacterial Proteins, chemistry; Binding Sites; Computational Biology, methods; Computer Simulation; Enzyme Inhibitors, chemistry; Hydrolases, antagonists /&/ inhibitors/chemistry; Models, Molecular; Models, Statistical; Molecular Structure; Pattern Recognition, Automated; Peptides, chemistry; Phylogeny; Protein Binding; Protein Conformation; Protein Interaction Mapping; Protein Structure, Tertiary; Proteins, chemistry; Streptomyces griseus, metabolism},
  Owner                    = {ranjan},
  Pii                      = {1471-2105-5-205},
  Pmid                     = {15606919},
  Timestamp                = {2009.12.05}
}

@Article{Sfatos1993,
  Title                    = {Phase diagram of random copolymers.},
  Author                   = {Sfatos and Gutin and Shakhnovich},
  Journal                  = {Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics},
  Year                     = {1993},

  Month                    = {Jul},
  Number                   = {1},
  Pages                    = {465--475},
  Volume                   = {48},

  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9960609},
  Timestamp                = {2011.11.28}
}

@Article{Shah2008,
  Title                    = {Oligo (N-aryl glycines): a new twist on structured peptoids},
  Author                   = {Shah, Neel H and Butterfoss, Glenn L and Nguyen, Khanh and Yoo, Barney and Bonneau, Richard and Rabenstein, Dallas L and Kirshenbaum, Kent},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {2008},
  Number                   = {49},
  Pages                    = {16622--16632},
  Volume                   = {130},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2014.06.11}
}

@Article{Shakhnovich1998,
  Title                    = {Protein design: a perspective from simple tractable models },
  Author                   = {Shakhnovich},
  Journal                  = {Fold Des},
  Year                     = {1998},
  Number                   = {3},
  Pages                    = {R45--R58},
  Volume                   = {3},

  Abstract                 = {Recent progress in computational approaches to protein design builds on advances in statistical mechanical protein folding theory. Here, the number of sequences folding into a given conformation is evaluated and a simple condition for a protein model's designability is outlined.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Shakhnovich1998.pdf:PDF},
  Institution              = {Harvard University Department of Chemistry and Chemical Biology 12 Oxford Street, Cambridge, MA 02138, USA eugene@belok.harvard.edu.},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9562552},
  Timestamp                = {2011.10.30}
}

@Article{Shakhnovich2006a,
  Title                    = {Relative contributions of structural designability and functional diversity in molecular evolution of duplicates.},
  Author                   = {Boris E Shakhnovich},
  Journal                  = {Bioinformatics},
  Year                     = {2006},

  Month                    = {Jul},
  Number                   = {14},
  Pages                    = {e440--e445},
  Volume                   = {22},

  Abstract                 = {Analysis of increasingly saturated sequence databases have shown that gene family sizes are highly skewed with many families being small and few containing many, far-diverged homologs. Additionally, recently published results have identified a structural determinant of mutational plasticity: designability that correlates strongly with gene family size. In this paper, we explore the possible links between the two observations, exploring the possible effect of designability on duplication and divergence. We show that designability has an inverse of expected relationship with strength of selection. More designable domains that should have more mutational plasticity evolve slower. However, we also present evidence that recently duplicated genes have variable probability of locus fixation correlated with strength of selection. As expected, paralogs under stronger evolutionary pressure have a lower failure rate. Finally, we show that probability of pseudogene formation from gene 
duplication can be directly tied to designability and functional flexibility of the family. We present evidence that gene families with higher designability have diverged farther because of lower probability of pseudogenization. Additionally, mutational plasticity may play an integral role by influencing pseudogenization rate. Either way, we show that considering the failure rate of duplications is integral in understanding the determinants and dynamics of molecular evolution.},
  Institution              = {Bioinformatics Program, 24 Cummington st., Boston University Boston, MA 02215, USA. borya@acs.bu.edu},
  Keywords                 = {Chromosome Mapping, methods; DNA Mutational Analysis, methods; Evolution, Molecular; Genes, Duplicate, genetics; Genetic Variation, genetics; Genetics, Population; Models, Genetic; Selection (Genetics)},
  Owner                    = {ranjan},
  Pii                      = {22/14/e440},
  Pmid                     = {16873505},
  Timestamp                = {2009.12.05}
}

@Article{Shakhnovich2005,
  Title                    = {Protein structure and evolutionary history determine sequence space topology.},
  Author                   = {Boris E Shakhnovich and Eric Deeds and Charles Delisi and Eugene Shakhnovich},
  Journal                  = {Genome Res},
  Year                     = {2005},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {385--392},
  Volume                   = {15},

  Abstract                 = {Understanding the observed variability in the number of homologs of a gene is a very important unsolved problem that has broad implications for research into coevolution of structure and function, gene duplication, pseudogene formation, and possibly for emerging diseases. Here, we attempt to define and elucidate some possible causes behind the observed irregularity in sequence space. We present evidence that sequence variability and functional diversity of a gene or fold family is influenced by quantifiable characteristics of the protein structure. These characteristics reflect the structural potential for sequence plasticity, i.e., the ability to accept mutation without losing thermodynamic stability. We identify a structural feature of a protein domain-contact density-that serves as a determinant of entropy in sequence space, i.e., the ability of a protein to accept mutations without destroying the fold (also known as fold designability). We show that (log) of average gene 
family size exhibits statistical correlation (R(2) > 0.9.) with contact density of its three-dimensional structure. We present evidence that the size of individual gene families are influenced not only by the designability of the structure, but also by evolutionary history, e.g., the amount of time the gene family was in existence. We further show that our observed statistical correlation between gene family size and contact density of the structure is valid on many levels of evolutionary divergence, i.e., not only for closely related sequence, but also for less-related fold and superfamily levels of homology.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Shakhnovich2005.pdf:PDF},
  Institution              = {Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA.},
  Keywords                 = {Amino Acid Sequence; Evolution, Molecular; Models, Genetic; Models, Molecular; Molecular Sequence Data; Mutation; Proteins, chemistry/genetics; Sequence Homology, Amino Acid; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {15/3/385},
  Pmid                     = {15741509},
  Timestamp                = {2009.12.05}
}

@Article{Shakhnovich2003,
  Title                    = {Functional fingerprints of folds: evidence for correlated structure-function evolution.},
  Author                   = {Boris E Shakhnovich and Nikolay V Dokholyan and Charles DeLisi and Eugene I Shakhnovich},
  Journal                  = {J Mol Biol},
  Year                     = {2003},

  Month                    = {Feb},
  Number                   = {1},
  Pages                    = {1--9},
  Volume                   = {326},

  Abstract                 = {Using structural similarity clustering of protein domains: protein domain universe graph (PDUG), and a hierarchical functional annotation: gene ontology (GO) as two evolutionary lenses, we find that each structural cluster (domain fold) exhibits a distribution of functions that is unique to it. These functional distributions are functional fingerprints that are specific to characteristic structural clusters and vary from cluster to cluster. Furthermore, as structural similarity threshold for domain clustering in the PDUG is relaxed we observe an influx of earlier-diverged domains into clusters. These domains join clusters without destroying the functional fingerprint. These results can be understood in light of a divergent evolution scenario that posits correlated divergence of structural and functional traits in protein domains from one or few progenitors.},
  Institution              = {Bioinformatics Program, Boston University, Boston, MA 02215, USA.},
  Keywords                 = {Adenosine Triphosphate, metabolism; Computational Biology, methods; Databases, Protein; Enzymes, chemistry/metabolism; Evolution, Molecular; Guanosine Triphosphate, metabolism; Protein Binding; Protein Folding; Protein Structure, Tertiary; Proteins, chemistry/metabolism; Proteomics, methods; Signal Transduction; Structure-Activity Relationship},
  Owner                    = {ranjan},
  Pii                      = {S0022283602013621},
  Pmid                     = {12547186},
  Timestamp                = {2009.12.05}
}

@Article{Shakhnovich2003a,
  Title                    = {ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations.},
  Author                   = {Boris E Shakhnovich and John M Harvey and Steve Comeau and David Lorenz and Charles DeLisi and Eugene Shakhnovich},
  Journal                  = {BMC Bioinformatics},
  Year                     = {2003},

  Month                    = {Sep},
  Pages                    = {34},
  Volume                   = {4},

  Abstract                 = {The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome organization that allow valid functional cross-annotation. However, these methods provide a lot of false negatives due to limited specificity inherent in the system. We want to create an evolutionarily inspired organization of data that would approach the issue of structure-function correlation from a new, probabilistic perspective. Such organization has possible applications in phylogeny, modeling of functional evolution and structural determination. ELISA (Evolutionary Lineage Inferred from Structural Analysis, http://romi.bu.edu/elisa) is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function "neighborhoods". The atomic unit of the database is a set of sequences and structural templates that 
those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). We introduce a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind.Availability: The database is available at http://romi.bu.edu/elisa.},
  Institution              = {BioInformatics Program, Boston University, Boston, MA, 02215, USA. borya@bu.edu},
  Keywords                 = {Amino Acid Sequence; Bacterial Proteins, chemistry/physiology; Computational Biology, methods/statistics /&/ numerical data; Databases, Protein, statistics /&/ numerical data; Evolution, Molecular; Internet; Models, Genetic; Models, Statistical; Molecular Sequence Data; Phylogeny; Protein Structure, Quaternary, physiology; Protein Structure, Tertiary, physiology; Sequence Homology, Amino Acid; Structure-Activity Relationship},
  Owner                    = {ranjan},
  Pii                      = {1471-2105-4-34},
  Pmid                     = {12952559},
  Timestamp                = {2009.12.05}
}

@Article{Shakhnovich2004,
  Title                    = {ELISA: a unified, multidimensional view of the protein domain universe.},
  Author                   = {Boris E Shakhnovich and John Max Harvey and Charles Delisi},
  Journal                  = {Genome Inform},
  Year                     = {2004},
  Number                   = {1},
  Pages                    = {213--220},
  Volume                   = {15},

  Abstract                 = {ELISA (http://romi.bu.edu/elisa/) is a database that was designed for flexibility in defining interesting queries about protein domain evolution. We have defined and included both the inherent characteristics of the domains such as structure and function and comparisons of these characteristics between domains. Thus, the database is useful in defining structural and functional links between related protein domains and by extension sequences that encode them. In this database we introduce and employ a novel method of functional annotation and comparison. For each protein domain we create a probabilistic functional annotation tree using GO. We have designed an algorithm that accurately compares these trees and thus provides a measure of "functional distance" between two protein domains. Along with functional annotation, we have also included structural comparison between protein domains and best sequence comparisons to all known genomes. The latter enables researchers to 
dynamically do searches for domains sharing similar phylogenetic profiles. This combination of data and tools enables the researcher to design complex queries to carry out research in the areas of protein domain evolution, structure prediction and functional annotation of novel sequences.},
  Institution              = {Bioinformatics Program, Boston University, 44 Cummigton St., Boston MA 02215, USA. borya@bu.edu},
  Keywords                 = {Amino Acid Sequence; Databases, Protein; Evolution, Molecular; Models, Genetic; Molecular Sequence Data; Phylogeny; Proteins, chemistry/genetics/metabolism},
  Owner                    = {ranjan},
  Pmid                     = {15712123},
  Timestamp                = {2009.12.05}
}

@Article{Shakhnovich2006,
  Title                    = {Origins and impact of constraints in evolution of gene families.},
  Author                   = {Boris E Shakhnovich and Eugene V Koonin},
  Journal                  = {Genome Res},
  Year                     = {2006},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {1529--1536},
  Volume                   = {16},

  Abstract                 = {Recent investigations of high-throughput genomic and phenomic data have uncovered a variety of significant but relatively weak correlations between a gene's functional and evolutionary characteristics. In particular, essential genes and genes with paralogs have a slight propensity to evolve more slowly than nonessential genes and singletons, respectively. However, given the weakness and multiplicity of these associations, their biological relevance remains uncertain. Here, we show that existence of an essential paralog can be used as a specific and strong gauge of selection. We partition gene families in several genomes into two classes: those that include at least one essential gene (E-families) and those without essential genes (N-families). We find that weaker purifying selection causes N-families to evolve in a more dynamic regime with higher rates both of duplicate fixation and pseudogenization. Because genes in E-families are subject to significantly stronger purifying 
selection than those in N-families, they survive longer and exhibit greater sequence divergence. Longer average survival time also allows for divergence of upstream regulatory regions, resulting in change of transcriptional context among paralogs in E-families. These findings are compatible with differential division of ancestral functions (subfunctionalization) or emergence of novel functions (neofunctionalization) being the prevalent modes of evolution of paralogs in E-families as opposed to pseudogenization (nonfunctionalization), which is the typical fate of paralogs in N-families. Unlike other characteristics of genes, such as essentiality, existence of paralogs, or expression level, membership in an E-family or an N-family strongly correlates with the level of selection and appears to be a major determinant of a gene's evolutionary fate.},
  Institution              = {Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA. Borya@acs.bu.edu},
  Keywords                 = {Animals; Caenorhabditis elegans, genetics; Databases, Genetic; Escherichia coli, genetics; Evolution, Molecular; Gene Duplication; Gene Expression; Genes, Bacterial; Genes, Essential; Genes, Fungal; Genes, Helminth; Multigene Family, genetics; Pseudogenes; ROC Curve; Saccharomyces cerevisiae, genetics; Selection (Genetics); Species Specificity; Transcription Factors, genetics},
  Owner                    = {ranjan},
  Pii                      = {gr.5346206},
  Pmid                     = {17053091},
  Timestamp                = {2009.12.05}
}

@Article{Shakhnovich2008,
  Title                    = {Improvisation in evolution of genes and genomes: whose structure is it anyway?},
  Author                   = {Boris E Shakhnovich and Eugene I Shakhnovich},
  Journal                  = {Curr Opin Struct Biol},
  Year                     = {2008},

  Month                    = {Jun},
  Number                   = {3},
  Pages                    = {375--381},
  Volume                   = {18},

  Abstract                 = {Significant progress has been made in recent years in a variety of seemingly unrelated fields such as sequencing, protein structure prediction, and high-throughput transcriptomics and metabolomics. At the same time, new microscopic models have been developed that made it possible to analyze the evolution of genes and genomes from first principles. The results from these efforts enable, for the first time, a comprehensive insight into the evolution of complex systems and organisms on all scales--from sequences to organisms and populations. Every newly sequenced genome uncovers new genes, families, and folds. Where do these new genes come from? How do gene duplication and subsequent divergence of sequence and structure affect the fitness of the organism? What role does regulation play in the evolution of proteins and folds? Emerging synergism between data and modeling provides first robust answers to these questions.},
  Institution              = {Department of Molecular and Cellular Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States.},
  Keywords                 = {Evolution; Gene Duplication; Genome; Proteins, genetics},
  Owner                    = {ranjan},
  Pii                      = {S0959-440X(08)00041-9},
  Pmid                     = {18487041},
  Timestamp                = {2009.12.05}
}

@Article{Shakhnovich2006b,
  Title                    = {Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.},
  Author                   = {Eugene Shakhnovich},
  Journal                  = {Chem Rev},
  Year                     = {2006},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {1559--1588},
  Volume                   = {106},

  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA. Shakhnovich@chemistry.harvard.edu},
  Keywords                 = {Algorithms; Evolution, Molecular; Kinetics; Models, Chemical; Models, Molecular; Molecular Structure; Phase Transition; Protein Engineering; Protein Folding; Proteins, chemistry; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {16683745},
  Timestamp                = {2009.12.05}
}

@Article{Shakhnovich1990b,
  Title                    = {Enumeration of all compact conformations of copolymers with random sequence links},
  Author                   = {E.I. Shakhnovich and A. Gutin},
  Journal                  = {J Chem Phys},
  Year                     = {1990},
  Pages                    = {5967-5971},
  Volume                   = {93},

  Owner                    = {ranjan},
  Timestamp                = {2011.11.03}
}

@Article{Shakhnovich1993,
  Title                    = {Engineering of stable and fast-folding sequences of model proteins.},
  Author                   = {E. I. Shakhnovich and A. M. Gutin},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1993},

  Month                    = {Aug},
  Number                   = {15},
  Pages                    = {7195--7199},
  Volume                   = {90},

  Abstract                 = {The statistical mechanics of protein folding implies that the best-folding proteins are those that have the native conformation as a pronounced energy minimum. We show that this can be obtained by proper selection of protein sequences and suggest a simple practical way to find these sequences. The statistical mechanics of these proteins with optimized native structure is discussed. These concepts are tested with a simple lattice model of a protein with full enumeration of compact conformations. Selected sequences are shown to have a native state that is very stable and kinetically accessible.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Shakhnovich1993.pdf:PDF},
  Institution              = {Department of Chemistry, Harvard University, Cambridge, MA 02138.},
  Keywords                 = {Kinetics; Models, Theoretical; Protein Conformation; Protein Engineering; Proteins, chemistry; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {8346235},
  Timestamp                = {2011.11.28}
}

@Article{Shakhnovich1991,
  Title                    = {Influence of point mutations on protein structure: probability of a neutral mutation.},
  Author                   = {E. I. Shakhnovich and A. M. Gutin},
  Journal                  = {J Theor Biol},
  Year                     = {1991},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {537--546},
  Volume                   = {149},

  Abstract                 = {We investigate the probability X that a random mutation (i.e. the substitution in a random site of one amino acid residue by randomly chosen residue) will be a neutral one, i.e. it will not lead to a change in structure. Using a random energy model for the description of protein energy "levels" we show that this probability depends only on stiffness of a chain which is characterized by the number of conformations per peptide bond gamma. The result is X approximately gamma -8. The application of this result for protein engineering experiments and for possible scenario of neutral evolution is discussed.},
  Institution              = {Institute of Protein Research, Academy of Sciences U.S.S.R., Puschino Moscow Region.},
  Keywords                 = {Mathematics; Models, Biological; Mutation; Protein Conformation; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {2062107},
  Timestamp                = {2009.12.05}
}

@Article{Shakhnovich1990,
  Title                    = {Implications of thermodynamics of protein folding for evolution of primary sequences.},
  Author                   = {E. I. Shakhnovich and A. M. Gutin},
  Journal                  = {Nature},
  Year                     = {1990},

  Month                    = {Aug},
  Number                   = {6286},
  Pages                    = {773--775},
  Volume                   = {346},

  Abstract                 = {Natural proteins exhibit essentially two-state thermodynamics, with one stable fold that dominates thermodynamically over a vast number of possible folds, a number that increases exponentially with the size of the protein. Here we address the question of whether this feature of proteins is a rare property selected by evolution or whether it is in fact true of a significant proportion of all possible protein sequences. Using statistical procedures developed to study spin glasses, we show that, given certain assumptions, the probability that a randomly synthesized protein chain will have a dominant fold (which is the global minimum of free energy) is a function of temperature, and that below a critical temperature the probability rapidly increases as the temperature decreases. Our results suggest that a significant proportion of all possible protein sequences could have a thermodynamically dominant fold.},
  File                     = {Shakhnovich1990.pdf:pdfs/Shakhnovich1990.pdf:PDF},
  Institution              = {Institute of Protein Research, Academy of Sciences of the USSR, Moscow Region.},
  Keywords                 = {Amino Acid Sequence; Evolution; Mathematics; Models, Theoretical; Probability; Protein Conformation; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {2388698},
  Timestamp                = {2009.12.05}
}

@Article{Shakhnovich1989,
  Title                    = {Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach.},
  Author                   = {E. I. Shakhnovich and A. M. Gutin},
  Journal                  = {Biophys Chem},
  Year                     = {1989},

  Month                    = {Nov},
  Number                   = {3},
  Pages                    = {187--199},
  Volume                   = {34},

  Abstract                 = {A replica approach analogous to that used in spin glass systems is implemented to study the configurational space of a heteropolymeric model of protein with a quenched, disordered sequence of links in the limit of a large number of link types. It is shown that there exists a threshold value of chain heterogeneity which separates two qualitatively different types of behavior. For a low degree of heterogeneity the protein globule is like a homopolymer in a collapsed state without definite chain folds: an exponentially large number of folds make a significant contribution to the partition function in this regime. After the threshold heterogeneity has been overcome, the chain freezes drastically but without latent heat; few (approx. 1) frozen states with definite chain folds are thermodynamically dominant in this state. The relation of these results to thermodynamic aspects of protein folding is discussed.},
  File                     = {Shakhnovich1989.pdf:pdfs/Shakhnovich1989.pdf:PDF},
  Institution              = {Institute of Protein Research, Academy of Sciences of the U.S.S.R., Moscow Region.},
  Keywords                 = {Mathematics; Models, Theoretical; Peptides; Protein Conformation; Proteins; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {0301-4622(89)80058-4},
  Pmid                     = {2611345},
  Timestamp                = {2010.01.18}
}

@Article{Shan2011,
  Title                    = {How does a drug molecule find its target binding site?},
  Author                   = {Shan, Yibing and Kim, Eric T and Eastwood, Michael P and Dror, Ron O and Seeliger, Markus A and Shaw, David E},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {2011},
  Number                   = {24},
  Pages                    = {9181--9183},
  Volume                   = {133},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2014.09.02}
}

@Article{Sharov2006,
  Title                    = {Genome increase as a clock for the origin and evolution of life.},
  Author                   = {Alexei A Sharov},
  Journal                  = {Biol Direct},
  Year                     = {2006},
  Pages                    = {17},
  Volume                   = {1},

  Abstract                 = {The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. Several positive feedback mechanisms including gene cooperation and duplication with subsequent specialization may result in the exponential growth of biological complexity in macro-evolution.I propose a hypothesis that biological complexity increased exponentially during evolution. Regression of the logarithm of functional non-redundant genome size versus time of origin in major groups of organisms showed a 7.8-fold increase per 1 billion years, and hence the increase of complexity can be viewed as a clock of macro-evolution. A strong version of the exponential hypothesis is that the rate of complexity increase in early (pre-prokaryotic) evolution of life was at most the same (or even slower) than observed in the evolution of prokaryotes and eukaryotes.The increase of functional non-redundant genome size in macro-evolution was consistent with the exponential hypothesis. 
If the strong exponential hypothesis is true, then the origin of life should be dated 10 billion years ago. Thus, the possibility of panspermia as a source of life on earth should be discussed on equal basis with alternative hypotheses of de-novo life origin. Panspermia may be proven if bacteria similar to terrestrial ones are found on other planets or satellites in the solar system.This article was reviewed by Eugene V. Koonin, Chris Adami and Arcady Mushegian.},
  Institution              = {Laboratory of Genetics, National Institute on Aging (NIA/NIH), 333 Cassell Dr,, Baltimore, MD 21224, USA.},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {1745-6150-1-17},
  Pmid                     = {16768805},
  Timestamp                = {2011.07.09}
}

@Article{Shepherd2006,
  Title                    = {VIPERdb: a relational database for structural virology},
  Author                   = {Shepherd, C. M. and Borelli, I. A. and Lander, G. and Natarajan, P. and Siddavanahalli, V. and Bajaj, C. and Johnson, J. E. and Brooks III, C. L. and Reddy, V. S.},
  Journal                  = {Nucl. Acids Res.},
  Year                     = {2006},
  Pages                    = {D386--D389},
  Volume                   = {34}
}

@Article{Shibaev1991,
  Title                    = {Odd-even effect and thermal stability in the series of vinyl polymers},
  Author                   = {Shibaev, L.A. and Stepanov, N.G. and Zuev, V.V. and Solovskaya, N.A. and Sazanov, Yu.N.},
  Journal                  = {Thermochimica Acta},
  Year                     = {1991},

  Month                    = {Sep},
  Number                   = {1},
  Pages                    = {19-34},
  Volume                   = {186},

  Doi                      = {10.1016/0040-6031(91)87019-S},
  Owner                    = {ranjan},
  Publisher                = {Elsevier },
  Timestamp                = {2014.01.17}
}

@Article{Shoemaker2000,
  Title                    = {Speeding molecular recognition by using the folding funnel: the fly-casting mechanism},
  Author                   = {Shoemaker, Benjamin A and Portman, John J and Wolynes, Peter G},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2000},
  Number                   = {16},
  Pages                    = {8868--8873},
  Volume                   = {97},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2013.11.21}
}

@Article{Shulman-Peleg2009,
  Title                    = {RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases.},
  Author                   = {Alexandra Shulman-Peleg and Ruth Nussinov and Haim J Wolfson},
  Journal                  = {Nucleic Acids Res},
  Year                     = {2009},

  Month                    = {Jan},
  Number                   = {Database issue},
  Pages                    = {D369--D373},
  Volume                   = {37},

  Abstract                 = {We present a new database and an on-line search engine, which store and query the protein binding pockets that interact with single-stranded RNA nucleotide bases. The database consists of a classification of binding sites derived from protein-RNA complexes. Each binding site is assigned to a cluster of similar binding sites in other protein-RNA complexes. Cluster members share similar spatial arrangements of physico-chemical properties, thus can reveal novel similarity between proteins and RNAs with different sequences and folds. The clusters provide 3D consensus binding patterns important for protein-nucleotide recognition. The database search engine allows two types of useful queries: first, given a PDB code of a protein-RNA complex, RsiteDB can detail and classify the properties of the protein binding pockets accommodating extruded RNA nucleotides not involved in local RNA base pairing. Second, given an unbound protein structure, RsiteDB can perform an on-line structural 
search against the constructed database of 3D consensus binding patterns. Regions similar to known patterns are predicted to serve as binding sites. Alignment of the query to these patterns with their corresponding RNA nucleotides allows making unique predictions of the protein-RNA interactions at the atomic level of detail. This database is accessible at http://bioinfo3d.cs.tau.ac.il/RsiteDB.},
  Institution              = {School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel. shulmana@post.tau.ac.il},
  Keywords                 = {Binding Sites; Databases, Protein; Protein Binding; RNA, chemistry; RNA-Binding Proteins, chemistry; Ribonucleotides, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {gkn759},
  Pmid                     = {18953028},
  Timestamp                = {2011.08.07}
}

@InCollection{Liu2012,
  Title                    = {Protein Folding, Binding and Energy Landscape: A Synthesis},
  Author                   = {Shu-Qun Liu, Xing-Lai Ji, Yan Tao, De-Yong Tan, Ke-Qin Zhang and Yun-Xin Fu},
  Booktitle                = {Protein Engineering},
  Publisher                = {InTech},
  Year                     = {2012},
  Editor                   = {Pravin Kaumaya},
  Pages                    = {207--252}
}

@Article{Sibille2012,
  Title                    = {Structural characterization of intrinsically disordered proteins by the combined use of NMR and SAXS.},
  Author                   = {Sibille, Nathalie and Bernado, Pau},
  Journal                  = {Biochemical society transactions},
  Year                     = {2012},
  Number                   = {5},
  Pages                    = {955--962},
  Volume                   = {40},

  Owner                    = {ranjan},
  Timestamp                = {2015.09.17}
}

@Article{Sikosek2012,
  Title                    = {Evolutionary dynamics on protein bi-stability landscapes can potentially resolve adaptive conflicts.},
  Author                   = {Sikosek, Tobias and Bornberg-Bauer, Erich and Chan, Hue Sun},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2012},
  Number                   = {9},
  Pages                    = {e1002659},
  Volume                   = {8},

  Abstract                 = {Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases 
gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149-21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed.},
  Institution              = {Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of M?nster, M?nster, Germany. sikosek@wwu.de},
  Keywords                 = {Adaptation, Physiological, genetics; Amino Acid Sequence; Computer Simulation; Evolution, Molecular; Genetic Variation, genetics; Models, Chemical; Models, Genetic; Molecular Sequence Data; Proteins, chemistry/genetics; Sequence Analysis, Protein, methods},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {PCOMPBIOL-D-12-00227},
  Pmid                     = {23028272},
  Timestamp                = {2013.06.13}
}

@Article{Sim2008,
  Title                    = {The core and accessory genomes of Burkholderia pseudomallei: implications for human melioidosis.},
  Author                   = {Sim, Siew Hoon and Yu, Yiting and Lin, Chi Ho and Karuturi, R Krishna M. and Wuthiekanun, Vanaporn and Tuanyok, Apichai and Chua, Hui Hoon and Ong, Catherine and Paramalingam, Sivalingam Suppiah and Tan, Gladys and Tang, Lynn and Lau, Gary and Ooi, Eng Eong and Woods, Donald and Feil, Edward and Peacock, Sharon J. and Tan, Patrick},
  Journal                  = {PLoS Pathog},
  Year                     = {2008},

  Month                    = {Oct},
  Number                   = {10},
  Pages                    = {e1000178},
  Volume                   = {4},

  Abstract                 = {Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, can exhibit significant ecological flexibility that is likely reflective of a dynamic genome. Using whole-genome Bp microarrays, we examined patterns of gene presence and absence across 94 South East Asian strains isolated from a variety of clinical, environmental, or animal sources. 86\% of the Bp K96243 reference genome was common to all the strains representing the Bp "core genome", comprising genes largely involved in essential functions (eg amino acid metabolism, protein translation). In contrast, 14\% of the K96243 genome was variably present across the isolates. This Bp accessory genome encompassed multiple genomic islands (GIs), paralogous genes, and insertions/deletions, including three distinct lipopolysaccharide (LPS)-related gene clusters. Strikingly, strains recovered from cases of human melioidosis clustered on a tree based on accessory gene content, and were significantly more 
likely to harbor certain GIs compared to animal and environmental isolates. Consistent with the inference that the GIs may contribute to pathogenesis, experimental mutation of BPSS2053, a GI gene, reduced microbial adherence to human epithelial cells. Our results suggest that the Bp accessory genome is likely to play an important role in microbial adaptation and virulence.},
  Institution              = {Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, Republic of Singapore.},
  Keywords                 = {Animals; Birds; Burkholderia pseudomallei, genetics/isolation /&/ purification/pathogenicity; Cluster Analysis; Dogs; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Gene Frequency; Genome, Bacterial; Genomic Islands; Haplorhini; Humans; INDEL Mutation; Melioidosis, genetics/microbiology/veterinary; Oligonucleotide Array Sequence Analysis; Phylogeny; Swine; Virulence Factors, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {18927621},
  Timestamp                = {2012.09.09}
}

@Article{Singer2000,
  Title                    = {Nucleotide bias causes a genomewide bias in the amino acid composition of proteins.},
  Author                   = {Singer, G. A. and Hickey, D. A.},
  Journal                  = {Mol Biol Evol},
  Year                     = {2000},

  Month                    = {Nov},
  Number                   = {11},
  Pages                    = {1581--1588},
  Volume                   = {17},

  Abstract                 = {We analyzed the nucleotide contents of several completely sequenced genomes, and we show that nucleotide bias can have a dramatic effect on the amino acid composition of the encoded proteins. By surveying the genes in 21 completely sequenced eubacterial and archaeal genomes, along with the entire Saccharomyces cerevisiae genome and two Plasmodium falciparum chromosomes, we show that biased DNA encodes biased proteins on a genomewide scale. The predicted bias affects virtually all genes within the genome, and it could be clearly seen even when we limited the analysis to sets of homologous gene sequences. Parallel patterns of compositional bias were found within the archaea and the eubacteria. We also found a positive correlation between the degree of amino acid bias and the magnitude of protein sequence divergence. We conclude that mutational bias can have a major effect on the molecular evolution of proteins. These results could have important implications for the interpretation 
of protein-based molecular phylogenies and for the inference of functional protein adaptation from comparative sequence data.},
  Institution              = {Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.},
  Keywords                 = {Amino Acids, genetics; Animals; Base Composition; Codon, genetics; Eukaryotic Cells, metabolism; Genetic Variation; Genome; Genome, Archaeal; Genome, Bacterial; Humans; Nucleotides, genetics; Phylogeny; Proteins, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {11070046},
  Timestamp                = {2012.09.27}
}

@Article{Singh2007,
  Title                    = {Role of intrinsic disorder in transient interactions of hub proteins.},
  Author                   = {Singh, Gajinder Pal and Ganapathi, Mythily and Dash, Debasis},
  Journal                  = {Proteins},
  Year                     = {2007},

  Month                    = {Mar},
  Number                   = {4},
  Pages                    = {761--765},
  Volume                   = {66},

  Abstract                 = {Hubs in the protein-protein interaction network have been classified as "party" hubs, which are highly correlated in their mRNA expression with their partners while "date" hubs show lesser correlation. In this study, we explored the role of intrinsic disorder in date and party hub interactions. The data reveals that intrinsic disorder is significantly enriched in date hub proteins when compared with party hub proteins. Intrinsic disorder has been largely implicated in transient binding interactions. The disorder to order transition, which occurs during binding interactions in disordered regions, renders the interaction highly reversible while maintaining the high specificity. The enrichment of intrinsic disorder in date hubs may facilitate transient interactions, which might be required for date hubs to interact with different partners at different times.},
  Institution              = {Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Delhi, India.},
  Keywords                 = {Computational Biology; Hu Paraneoplastic Encephalomyelitis Antigens, chemistry/metabolism; Protein Binding; Protein Structure, Secondary},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {17154416},
  Timestamp                = {2012.09.26}
}

@Article{Slade2011,
  Title                    = {The self-avoiding walk: a brief survey},
  Author                   = {Slade, Gordon},
  Journal                  = {Surveys in Stochastic Processes},
  Year                     = {2011},
  Pages                    = {181--199},

  Owner                    = {ranjan},
  Publisher                = {European Mathematical Society},
  Timestamp                = {2014.08.27}
}

@Article{Slade1994,
  Title                    = {Self-avoiding walks},
  Author                   = {Slade, Gordon},
  Journal                  = {The Mathematical Intelligencer},
  Year                     = {1994},
  Number                   = {1},
  Pages                    = {29--35},
  Volume                   = {16},

  Owner                    = {ranjan},
  Publisher                = {Springer},
  Timestamp                = {2016.06.18}
}

@Article{Smith2007,
  Title                    = {The hitch-hiking effect of a favourable gene.},
  Author                   = {John Maynard Smith and John Haigh},
  Journal                  = {Genet Res},
  Year                     = {2007},

  Month                    = {Dec},
  Number                   = {5-6},
  Pages                    = {391--403},
  Volume                   = {89},

  Institution              = {University of Sussex, Brighton.},
  Owner                    = {ranjan},
  Pii                      = {S0016672308009579},
  Pmid                     = {18976527},
  Timestamp                = {2011.05.02}
}

@Article{Smith1974,
  Title                    = {The hitch-hiking effect of a favourable gene.},
  Author                   = {J. M. Smith and J. Haigh},
  Journal                  = {Genet Res},
  Year                     = {1974},

  Month                    = {Feb},
  Number                   = {1},
  Pages                    = {23--35},
  Volume                   = {23},

  Keywords                 = {Alleles; Animals; Gene Frequency; Genetics, Population; Heterozygote; Humans; Polymorphism, Genetic; Probability; Selection, Genetic},
  Owner                    = {ranjan},
  Pmid                     = {4407212},
  Timestamp                = {2011.05.02}
}

@Article{Smith2009,
  Title                    = {Life history influences rates of climatic niche evolution in flowering plants.},
  Author                   = {Stephen A Smith and Jeremy M Beaulieu},
  Journal                  = {Proc Biol Sci},
  Year                     = {2009},

  Month                    = {Dec},
  Number                   = {1677},
  Pages                    = {4345--4352},
  Volume                   = {276},

  Abstract                 = {Across angiosperms, variable rates of molecular substitution are linked with life-history attributes associated with woody and herbaceous growth forms. As the number of generations per unit time is correlated with molecular substitution rates, it is expected that rates of phenotypic evolution would also be influenced by differences in generation times. Here, we make the first broad-scale comparison of growth-form-dependent rates of niche evolution. We examined the climatic niches of species on large time-calibrated phylogenies of five angiosperm clades and found that woody lineages have accumulated fewer changes per million years in climatic niche space than related herbaceous lineages. Also, climate space explored by woody lineages is consistently smaller than sister lineages composed mainly of herbaceous taxa. This pattern is probably linked to differences in the rate of climatic niche evolution. These results have implications for niche conservatism; in particular, the role 
of niche conservatism in the distribution of plant biodiversity. The consistent differences in the rate of climatic niche evolution also emphasize the need to incorporate models of phenotypic evolution that allow for rate heterogeneity when examining large datasets.},
  Institution              = {National Evolutionary Synthesis Center, 2024 W. Main Street A200, Durham, NC 27705, USA. sasmith@nescent.org},
  Keywords                 = {Adaptation, Biological, genetics/physiology; Analysis of Variance; Angiosperms, growth /&/ development; Biological Evolution; Climate; Ecosystem; Phylogeny; Principal Component Analysis; Species Specificity},
  Owner                    = {ranjan},
  Pii                      = {rspb.2009.1176},
  Pmid                     = {19776076},
  Timestamp                = {2011.04.27}
}

@Article{Smith2008,
  Title                    = {Rates of molecular evolution are linked to life history in flowering plants.},
  Author                   = {Stephen A Smith and Michael J Donoghue},
  Journal                  = {Science},
  Year                     = {2008},

  Month                    = {Oct},
  Number                   = {5898},
  Pages                    = {86--89},
  Volume                   = {322},

  Abstract                 = {Variable rates of molecular evolution have been documented across the tree of life, but the cause of this observed variation within and among clades remains uncertain. In plants, it has been suggested that life history traits are correlated with the rate of molecular evolution, but previous studies have yielded conflicting results. Exceptionally large phylogenies of five major angiosperm clades demonstrate that rates of molecular evolution are consistently low in trees and shrubs, with relatively long generation times, as compared with related herbaceous plants, which generally have shorter generation times. Herbs show much higher rates of molecular change but also much higher variance in rates. Correlates of life history attributes have long been of interest to biologists, and our results demonstrate how changes in the rate of molecular evolution that are linked to life history traits can affect measurements of the tempo of evolution as well as our ability to identify and 
conserve biodiversity.},
  Institution              = {Department of Ecology and Evolutionary Biology, 21 Sachem Street, Post Office Box 208105, Yale University, New Haven, CT 06520-8105, USA. stephen.smith@yale.edu},
  Keywords                 = {Angiosperms, classification/genetics/growth /&/ development; Evolution, Molecular; Flowers, growth /&/ development; Genes, Plant; Phylogeny; Trees, genetics/growth /&/ development},
  Owner                    = {ranjan},
  Pii                      = {322/5898/86},
  Pmid                     = {18832643},
  Timestamp                = {2011.04.27}
}

@Article{Snel2002,
  Title                    = {Genomes in flux: the evolution of archaeal and proteobacterial gene content.},
  Author                   = {Snel, Berend and Bork, Peer and Huynen, Martijn A.},
  Journal                  = {Genome Res},
  Year                     = {2002},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {17--25},
  Volume                   = {12},

  Abstract                 = {In the course of evolution, genomes are shaped by processes like gene loss, gene duplication, horizontal gene transfer, and gene genesis (the de novo origin of genes). Here we reconstruct the gene content of ancestral Archaea and Proteobacteria and quantify the processes connecting them to their present day representatives based on the distribution of genes in completely sequenced genomes. We estimate that the ancestor of the Proteobacteria contained around 2500 genes, and the ancestor of the Archaea around 2050 genes. Although it is necessary to invoke horizontal gene transfer to explain the content of present day genomes, gene loss, gene genesis, and simple vertical inheritance are quantitatively the most dominant processes in shaping the genome. Together they result in a turnover of gene content such that even the lineage leading from the ancestor of the Proteobacteria to the relatively large genome of Escherichia coli has lost at least 950 genes. Gene loss, unlike the other 
processes, correlates fairly well with time. This clock-like behavior suggests that gene loss is under negative selection, while the processes that add genes are under positive selection.},
  Institution              = {European Molecular Biology Laboratory, 69117 Heidelberg, Germany. snel@EMBL-heidelberg.de},
  Keywords                 = {Amino Acid Substitution, genetics; Archaea, genetics; Bacteria, genetics; Evolution, Molecular; Gene Deletion; Gene Duplication; Gene Transfer, Horizontal, genetics; Genes, Archaeal, genetics; Genes, Bacterial, genetics; Genome, Archaeal; Genome, Bacterial; Models, Genetic; Mutagenesis, genetics; Phylogeny; Proteobacteria, genetics; Recombination, Genetic, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {11779827},
  Timestamp                = {2012.09.06}
}

@Article{Snow2002,
  Title                    = {Absolute comparison of simulated and experimental protein-folding dynamics.},
  Author                   = {Snow, Christopher D. and Nguyen, Houbi and Pande, Vijay S. and Gruebele, Martin},
  Journal                  = {Nature},
  Year                     = {2002},

  Month                    = {Nov},
  Number                   = {6911},
  Pages                    = {102--106},
  Volume                   = {420},

  Abstract                 = {Protein folding is difficult to simulate with classical molecular dynamics. Secondary structure motifs such as alpha-helices and beta-hairpins can form in 0.1-10 micros (ref. 1), whereas small proteins have been shown to fold completely in tens of microseconds. The longest folding simulation to date is a single 1- micro s simulation of the villin headpiece; however, such single runs may miss many features of the folding process as it is a heterogeneous reaction involving an ensemble of transition states. Here, we have used a distributed computing implementation to produce tens of thousands of 5-20-ns trajectories (700 micros) to simulate mutants of the designed mini-protein BBA5. The fast relaxation dynamics these predict were compared with the results of laser temperature-jump experiments. Our computational predictions are in excellent agreement with the experimentally determined mean folding times and equilibrium constants. The rapid folding of BBA5 is due to the swift 
formation of secondary structure. The convergence of experimentally and computationally accessible timescales will allow the comparison of absolute quantities characterizing in vitro and in silico (computed) protein folding.},
  Institution              = {Biophysics Program and Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.},
  Keywords                 = {Amino Acid Sequence; Circular Dichroism; Computer Simulation; Kinetics; Lasers; Models, Molecular; Molecular Sequence Data; Mutation; Protein Engineering; Protein Folding; Protein Structure, Secondary; Proteins, chemistry/genetics/metabolism; Spectrometry, Fluorescence; Temperature; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nature01160},
  Pmid                     = {12422224},
  Timestamp                = {2012.07.14}
}

@Article{Song2008,
  Title                    = {A phase diagram for jammed matter},
  Author                   = {Song, Chaoming and Wang, Ping and Makse, Hern{\'a}n A},
  Journal                  = {Nature},
  Year                     = {2008},
  Number                   = {7195},
  Pages                    = {629--632},
  Volume                   = {453},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2015.06.29}
}

@Article{Soskine2010,
  Title                    = {Mutational effects and the evolution of new protein functions.},
  Author                   = {Misha Soskine and Dan S Tawfik},
  Journal                  = {Nature genetics},
  Year                     = {2010},
  Pages                    = {572},
  Volume                   = {11},

  Owner                    = {ranjan},
  Timestamp                = {2010.09.02}
}

@Article{Spearman1904,
  Title                    = {The proof and measurement of association between two things},
  Author                   = {C. Spearman},
  Journal                  = {Am J Psychol},
  Year                     = {1904},
  Number                   = {1},
  Pages                    = {72--101},
  Volume                   = {15},

  Keywords                 = {History, 20th Century; Psychology, Experimental, history; Psychometrics, history; United States},
  Owner                    = {ranjan},
  Pmid                     = {3322052},
  Timestamp                = {2010.09.24}
}

@Article{Speijer2011,
  Title                    = {Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity.},
  Author                   = {Dave Speijer},
  Journal                  = {Bioessays},
  Year                     = {2011},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {344--349},
  Volume                   = {33},

  Abstract                 = {Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to 'overselectionism'. Here I contend, that in its extended form, it has major conceptual problems, can not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and--if seen as a major evolutionary mechanism for all organisms--could stifle further thought regarding the evolution of highly complex biological processes.},
  Institution              = {Academic Medical Center (AMC), Department of Medical Biochemistry, University of Amsterdam, Amsterdam, The Netherlands. d.speijer@amc.uva.nl},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {21381061},
  Timestamp                = {2011.08.05}
}

@Article{Stachelhaus1998,
  Title                    = {Peptide bond formation in nonribosomal peptide biosynthesis. Catalytic role of the condensation domain.},
  Author                   = {T. Stachelhaus and H. D. Mootz and V. Bergendahl and M. A. Marahiel},
  Journal                  = {J Biol Chem},
  Year                     = {1998},

  Month                    = {Aug},
  Number                   = {35},
  Pages                    = {22773--22781},
  Volume                   = {273},

  Abstract                 = {Recently, considerable insight has been gained into the modular organization and catalytic properties of nonribosomal peptide synthetases. However, molecular and biochemical aspects of the condensation of two aminoacyl substrates or a peptidyl and an aminoacyl substrate, leading to the formation of a peptide bond, have remained essentially impenetrable. To investigate this crucial part of nonribosomal peptide synthesis, an in vitro assay for a dipeptide formation was developed. Two recombinant holomodules, GrsA (PheATE), providing D-Phe, and a C-terminally truncated TycB, corresponding to the first, L-Pro-incorporating module (ProCAT), were investigated. Upon combination of the two aminoacylated modules, a fast reaction is observed, due to the formation of the linear dipeptide D-Phe-L-Pro-S-enzyme on ProCAT, followed by a noncatalyzed release of the dipeptide from the enzyme. The liberated product was identified by TLC, high pressure liquid chromatography-mass spectrometry, 1H 
and 13C NMR, and comparison with a chemically synthesized standard to be the expected D-Phe-L-Pro diketopiperazine. Further minimization of the two modules was not possible without a loss of transfer activity. Likewise, a mutation in a proposed active-site motif (HHXXXDG) of the condensation domain giving ProCAT(H147V), abolished the condensation reaction. These results strongly suggest the condensation domain to be involved in the catalysis of nonribosomal peptide bond formation with the histidine 147 playing a catalytic role.},
  Institution              = {Biochemie/Fachbereich Chemie, Philipps-Universit?t Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany.},
  Keywords                 = {Amino Acid Sequence; Catalysis; Chromatography, High Pressure Liquid, methods; Chromatography, Thin Layer; Cloning, Molecular; Magnetic Resonance Spectroscopy; Mass Spectrometry, methods; Peptide Biosynthesis; Peptide Synthases, chemistry/genetics/isolation /&/ purification; Peptides, chemistry; Recombinant Proteins, biosynthesis/metabolism; Ribosomal Proteins, chemistry},
  Owner                    = {ranjan},
  Pmid                     = {9712910},
  Timestamp                = {2010.02.08}
}

@Article{Staneva2012,
  Title                    = {Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study},
  Author                   = {Staneva, Iskra and Huang, Yongqi and Liu, Zhirong and Wallin, Stefan},
  Year                     = {2012},

  Owner                    = {ranjan},
  Timestamp                = {2015.09.17}
}

@Article{Steenkamp2006,
  Title                    = {The protistan origins of animals and fungi.},
  Author                   = {Emma T Steenkamp and Jane Wright and Sandra L Baldauf},
  Journal                  = {Mol Biol Evol},
  Year                     = {2006},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {93--106},
  Volume                   = {23},

  Abstract                 = {Recent molecular studies suggest that Opisthokonta, the eukaryotic supergroup including animals and fungi, should be expanded to include a diverse collection of primitively single-celled eukaryotes previously classified as Protozoa. These taxa include corallochytreans, nucleariids, ministeriids, choanoflagellates, and ichthyosporeans. Assignment of many of these taxa to Opisthokonta remains uncorroborated as it is based solely on small subunit ribosomal RNA trees lacking resolution and significant bootstrap support for critical nodes. Therefore, important details of the phylogenetic relationships of these putative opisthokonts with each other and with animals and fungi remain unclear. We have sequenced elongation factor 1-alpha (EF-1alpha), actin, beta-tubulin, and HSP70, and/or alpha-tubulin from representatives of each of the proposed protistan opisthokont lineages, constituting the first protein-coding gene data for some of them. Our results show that members of all 
opisthokont protist groups encode a approximately 12-amino acid insertion in EF-1alpha, previously found exclusively in animals and fungi. Phylogenetic analyses of combined multigene data sets including a diverse set of opisthokont and nonopisthokont taxa place all of the proposed opisthokont protists unequivocally in an exclusive clade with animals and fungi. Within this clade, the nucleariid appears as the closest sister taxon to fungi, while the corallochytrean and ichthyosporean form a group which, together with the ministeriid and choanoflagellates, form two to three separate sister lineages to animals. These results further establish Opisthokonta as a bona fide taxonomic group and suggest that any further testing of the legitimacy of this taxon should, at the least, include data from opisthokont protists. Our results also underline the critical position of these "animal-fungal allies" with respect to the origin and early evolution of animals and fungi.},
  Institution              = {Department of Biology, University of York, Heslington, York, United Kingdom.},
  Keywords                 = {Actins, genetics; Amino Acid Sequence; Animals; Base Sequence; Bayes Theorem; Conserved Sequence, genetics; DNA Primers; Evolution, Molecular; Fungi, genetics; HSP70 Heat-Shock Proteins, genetics; Likelihood Functions; Models, Genetic; Molecular Sequence Data; Peptide Elongation Factor 1, genetics; Phylogeny; Protozoa, genetics; Sequence Alignment; Sequence Analysis, DNA; Tubulin, genetics},
  Owner                    = {ranjan},
  Pii                      = {msj011},
  Pmid                     = {16151185},
  Timestamp                = {2009.11.27}
}

@Article{Stehle1996,
  Title                    = {The structure of simian virus 40 refined at 3.1 A resolution.},
  Author                   = {Stehle, T. and Gamblin, S. J. and Yan, Y. and Harrison, S. C.},
  Journal                  = {Structure.},
  Year                     = {1996},
  Number                   = {2},
  Pages                    = {165--182},
  Volume                   = {4},

  File                     = {Stehle1996.pdf:pdfs/Stehle1996.pdf:PDF}
}

@Article{Stein1985,
  Title                    = {A model of protein conformational substates.},
  Author                   = {D. L. Stein},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1985},

  Month                    = {Jun},
  Number                   = {11},
  Pages                    = {3670--3672},
  Volume                   = {82},

  Abstract                 = {Many proteins have been observed to exist in a large number of conformations that are believed to play an important role in their dynamics. A model of protein conformational substates that incorporates the ideas of frustration and disorder in analogy to glasses and spin glasses is proposed. Applications to x-ray diffraction, M?ssbauer studies, and recombination experiments are discussed.},
  File                     = {Stein1985.pdf:pdfs/Stein1985.pdf:PDF},
  Institution              = {Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544.},
  Owner                    = {ranjan},
  Pmid                     = {16593568},
  Timestamp                = {2010.01.19}
}

@Article{Steitz2008,
  Title                    = {A structural understanding of the dynamic ribosome machine.},
  Author                   = {Steitz, Thomas A.},
  Journal                  = {Nat Rev Mol Cell Biol},
  Year                     = {2008},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {242--253},
  Volume                   = {9},

  Abstract                 = {Ribosomes, which are central to protein synthesis and convert transcribed mRNAs into polypeptide chains, have been the focus of structural and biochemical studies for more than 50 years. The structure of its larger subunit revealed that the ribosome is a ribozyme with RNA at the heart of its enzymatic activity that catalyses peptide bond formation. Numerous initiation, elongation and release factors ensure that protein synthesis occurs progressively and with high specificity. In the past few years, high-resolution structures have provided molecular snapshots of different intermediates in ribosome-mediated translation in atomic detail. Together, these studies have revolutionized our understanding of the mechanism of protein synthesis.},
  Institution              = {Department of Molecular Biophysics and Biochemistry, Department of Chemistry, Yale University, and the Howard Hughes Medical Institute, New Haven, Connecticut 06520-8114, USA. peggy.eatherton@yale.edu},
  Keywords                 = {Aminoacylation; Animals; Catalysis; Humans; Protein Biosynthesis; RNA, Messenger, chemistry/metabolism; RNA, Transfer, Ala, chemistry/metabolism; Ribosomes, chemistry/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nrm2352},
  Pmid                     = {18292779},
  Timestamp                = {2012.04.06}
}

@Article{Stephens1994,
  Title                    = {Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields},
  Author                   = {Stephens, PJ and Devlin, FJ and Chabalowski, CF and Frisch, Michael J},
  Journal                  = {The Journal of Physical Chemistry},
  Year                     = {1994},
  Number                   = {45},
  Pages                    = {11623--11627},
  Volume                   = {98},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2014.07.23}
}

@Article{Stetter2006,
  Title                    = {Hyperthermophiles in the history of life.},
  Author                   = {Stetter, Karl O.},
  Journal                  = {Philos Trans R Soc Lond B Biol Sci},
  Year                     = {2006},

  Month                    = {Oct},
  Number                   = {1474},
  Pages                    = {1837--42; discussion 1842-3},
  Volume                   = {361},

  Abstract                 = {Today, hyperthermophilic ('superheat-loving') bacteria and archaea are found within high-temperature environments, representing the upper temperature border of life. They grow optimally above 80 degrees C and exhibit an upper temperature border of growth up to 113 degrees C. Members of the genera, Pyrodictium and Pyrolobus, survive at least 1h of autoclaving. In their basically anaerobic environments, hyperthermophiles (HT) gain energy by inorganic redox reactions employing compounds like molecular hydrogen, carbon dioxide, sulphur and ferric and ferrous iron. Based on their growth requirements, HT could have existed already on the early Earth about 3.9Gyr ago. In agreement, within the phylogenetic tree of life, they occupy all the short deep branches closest to the root. The earliest archaeal phylogenetic lineage is represented by the extremely tiny members of the novel kingdom of Nanoarchaeota, which thrive in submarine hot vents. HT are very tough survivors, even in deep-
freezing at -140 degrees C. Therefore, during impact ejecta, they could have been successfully transferred to other planets and moons through the coldness of space.},
  Institution              = {University of Regensburg, Universit{\"a}tsstrasse 31, 93053 Regensburg, Germany. karl.setter@biologie.uni-regensburg.de},
  Keywords                 = {Archaea, genetics/physiology; Bacteria, genetics/metabolism; Biogenesis; Biological Evolution; Ecosystem; Hot Temperature},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {20410744H1L331W0},
  Pmid                     = {17008222},
  Timestamp                = {2012.04.06}
}

@Article{Stillinger1988,
  Title                    = {Dynamical lattice gases and inherent structure in condensed phases},
  Author                   = {Stillinger, FH},
  Journal                  = {The Journal of chemical physics},
  Year                     = {1988},
  Number                   = {1},
  Pages                    = {380--385},
  Volume                   = {88},

  Owner                    = {ranjan},
  Publisher                = {AIP Publishing},
  Timestamp                = {2015.09.22}
}

@Article{Stillinger1983,
  Title                    = {Inherent structure in water},
  Author                   = {Stillinger, Frank H and Weber, Thomas A},
  Journal                  = {The Journal of Physical Chemistry},
  Year                     = {1983},
  Number                   = {15},
  Pages                    = {2833--2840},
  Volume                   = {87},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2015.06.29}
}

@Article{Straight2007,
  Title                    = {A singular enzymatic megacomplex from Bacillus subtilis.},
  Author                   = {Straight, Paul D. and Fischbach, Michael A. and Walsh, Christopher T. and Rudner, David Z. and Kolter, Roberto},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2007},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {305--310},
  Volume                   = {104},

  Abstract                 = {Nonribosomal peptide synthetases (NRPS), polyketide synthases (PKS), and hybrid NRPS/PKS are of particular interest, because they produce numerous therapeutic agents, have great potential for engineering novel compounds, and are the largest enzymes known. The predicted masses of known enzymatic assembly lines can reach almost 5 megadaltons, dwarfing even the ribosome (approximately 2.6 megadaltons). Despite their uniqueness and importance, little is known about the organization of these enzymes within the native producer cells. Here we report that an 80-kb gene cluster, which occupies approximately 2\% of the Bacillus subtilis genome, encodes the subunits of approximately 2.5 megadalton active hybrid NRPS/PKS. Many copies of the NRPS/PKS assemble into a single organelle-like membrane-associated complex of tens to hundreds of megadaltons. Such an enzymatic megacomplex is unprecedented in bacterial subcellular organization and has important implications for engineering novel NRPS/
PKSs.},
  Institution              = {Department of Microbiology and Molecular Genetics and Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.},
  Keywords                 = {Amino Acid Sequence; Bacillus subtilis, enzymology/genetics; Cryoelectron Microscopy; Molecular Sequence Data; Multigene Family; Peptide Synthases, genetics; Polyketide Synthases, genetics; Protein Engineering},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {0609073103},
  Pmid                     = {17190806},
  Timestamp                = {2012.04.06}
}

@Article{Straub1967,
  Title                    = {SH groups and SS bridges in the structure of enzymes},
  Author                   = {Straub, FB},
  Journal                  = {Proc 7th Int Congr Biochem Tokyo},
  Year                     = {1967},
  Pages                    = {41--50},

  Owner                    = {ranjan},
  Timestamp                = {2013.11.18}
}

@InBook{Straub1964,
  Title                    = {Molecular Biology: Problems and Perspectives},
  Author                   = {F. B. Straub and G. Szabolcsi},
  Chapter                  = {Remarks on the dynamic aspects of enzyme structure (in russian)},
  Editor                   = {A. E. Braunstein},
  Pages                    = {182--187},
  Publisher                = {Nauka, Moscow},
  Year                     = {1964},

  Owner                    = {ranjan},
  Timestamp                = {2013.11.18}
}

@Article{Stray2005,
  Title                    = {A heteroaryldihydropyrimidine activates and can misdirect hepatitis B virus capsid assembly},
  Author                   = {Stray, S.J. and Bourne, C. and Punna, S. and Lewis, W.G. and Finn, M.G. and Zlotnick, A.},
  Journal                  = PNAS,
  Year                     = {2005},
  Pages                    = {8138--8143},
  Volume                   = {102},

  File                     = {Stray2005.pdf:pdfs/Stray2005.pdf:PDF}
}

@Article{Stray2006,
  Title                    = {BAY41-4109 has Multiple Effects on Hepatitis B Virus Capsid Assembly.},
  Author                   = {Stray, S.J. and Zlotnick, A.},
  Journal                  = {J. Mol. Recog. },
  Year                     = {2006},
  Pages                    = {542--548},
  Volume                   = {19},

  File                     = {Stray2006.pdf:pdfs/Stray2006.pdf:PDF}
}

@Article{Strieker2010,
  Title                    = {Nonribosomal peptide synthetases: structures and dynamics},
  Author                   = {Strieker, Matthias and Tanovi{\'c}, Alan and Marahiel, Mohamed A},
  Journal                  = {Current opinion in structural biology},
  Year                     = {2010},
  Number                   = {2},
  Pages                    = {234--240},
  Volume                   = {20},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.07.28}
}

@Article{Stringer2010,
  Title                    = {Construction of peptoids with all trans-amide backbones and peptoid reverse turns via the tactical incorporation of N-aryl side chains capable of hydrogen bonding},
  Author                   = {Stringer, Joseph R and Crapster, J Aaron and Guzei, Ilia A and Blackwell, Helen E},
  Journal                  = {The Journal of organic chemistry},
  Year                     = {2010},
  Number                   = {18},
  Pages                    = {6068--6078},
  Volume                   = {75},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2014.07.23}
}

@Article{Stumpf2008,
  Title                    = {Estimating the size of the human interactome.},
  Author                   = {Michael P H Stumpf and Thomas Thorne and Eric de Silva and Ronald Stewart and Hyeong Jun An and Michael Lappe and Carsten Wiuf},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2008},

  Month                    = {May},
  Number                   = {19},
  Pages                    = {6959--6964},
  Volume                   = {105},

  Abstract                 = {After the completion of the human and other genome projects it emerged that the number of genes in organisms as diverse as fruit flies, nematodes, and humans does not reflect our perception of their relative complexity. Here, we provide reliable evidence that the size of protein interaction networks in different organisms appears to correlate much better with their apparent biological complexity. We develop a stable and powerful, yet simple, statistical procedure to estimate the size of the whole network from subnet data. This approach is then applied to a range of eukaryotic organisms for which extensive protein interaction data have been collected and we estimate the number of interactions in humans to be approximately 650,000. We find that the human interaction network is one order of magnitude bigger than the Drosophila melanogaster interactome and approximately 3 times bigger than in Caenorhabditis elegans.},
  File                     = {Stumpf2008.pdf:pdfs/Stumpf2008.pdf:PDF},
  Institution              = {Division of Molecular Biosciences, Imperial College London, Wolfson Building, London SW7 2AZ, United Kingdom. m.stumpf@imperial.ac.uk},
  Keywords                 = {Animals; Caenorhabditis elegans, metabolism; Databases, Protein; Drosophila melanogaster, metabolism; Humans; Protein Interaction Mapping; Saccharomyces cerevisiae, metabolism},
  Owner                    = {ranjan},
  Pii                      = {0708078105},
  Pmid                     = {18474861},
  Timestamp                = {2011.03.03}
}

@Article{Sturtevant1944,
  Title                    = {Can Specific Mutations Be Induced by Serological Methods?},
  Author                   = {Sturtevant, Alfred H},
  Journal                  = {Proceedings of the National Academy of Sciences of the United States of America},
  Year                     = {1944},
  Number                   = {8},
  Pages                    = {176},
  Volume                   = {30},

  Owner                    = {ranjan},
  Publisher                = {National Academy of Sciences},
  Timestamp                = {2013.12.03}
}

@Article{Subramanian2001,
  Title                    = {GN Ramachandran},
  Author                   = {Subramanian, Easwara},
  Journal                  = {Nature Structural \& Molecular Biology},
  Year                     = {2001},
  Number                   = {6},
  Pages                    = {489--491},
  Volume                   = {8},

  Publisher                = {Nature Publishing Group}
}

@Article{Subramanian2011,
  Title                    = {Time dependency of molecular evolutionary rates? Yes and no.},
  Author                   = {Subramanian, Sankar and Lambert, David M.},
  Journal                  = {Genome Biol Evol},
  Year                     = {2011},
  Pages                    = {1324--1328},
  Volume                   = {3},

  Abstract                 = {Some previous studies have suggested that rates of evolution inferred using molecular sequences vary substantially depending on the time frame over which they are measured, whereas a number of other studies have argued against this proposition. We examined this issue by separating positions of primate mitochondrial genomes that are under different levels of selection constraints. Our results revealed an order of magnitude variation in the evolutionary rates at constrained sites (including nonsynonymous sites, D-loop, and RNA) and virtually an identical rate of evolution at synonymous sites, independent of the timescales over which they were estimated. Although the evolutionary rate at nonsynonymous sites obtained using the European (H1 haplogroup) mitogenomes is 9-15 times higher than that estimated using the human-chimpanzee pair, in contrast, the rates at synonymous sites are similar between these comparisons. We also show that the ratio of divergence at nonsynonymous to 
synonymous sites estimated using intra- and interspecific comparisons vary up to nine times, which corroborates our results independent of calibration times.},
  Keywords                 = {Animals; DNA, Mitochondrial, genetics; Evolution, Molecular; Genome, Mitochondrial, genetics; Hominidae, genetics; Humans; Neanderthals, genetics; Pan troglodytes, genetics; Phylogeny},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {evr108},
  Pmid                     = {22016336},
  Timestamp                = {2012.09.09}
}

@Article{Subramanya1993,
  Title                    = {Structure of Sesbania mosaic virus at 4.7 A resolution and partial sequence of the coat protein.},
  Author                   = {Subramanya, H.S. and Gopinath, K. and Nayudu, M.V. and Savithri, H.S. and Murthy, M.R.},
  Journal                  = JMB,
  Year                     = {1993},
  Number                   = {1},
  Pages                    = {20--25},
  Volume                   = {229},

  File                     = {Subramanya1993.pdf:pdfs/Subramanya1993.pdf:PDF}
}

@Article{Sue2015,
  Title                    = {Two-component metal-organic framework displaying compositional robustness to solution constitution.},
  Author                   = {Andrew C.-H. Sue and Ranjan V. Mannige and Hexiang Deng and Dennis Cao and Cheng Wang and Felipe G\'andaraa and Fraser Stoddart and Stephen Whitelamc and Omar M. Yaghi},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2015},
  Number                   = {18},
  Pages                    = {5591--5596},
  Volume                   = {112},

  Owner                    = {ranjan},
  Timestamp                = {2014.08.14}
}

@Article{Sueoka1962,
  Title                    = {On the genetic basis of variation and heterogeneity of DNA base composition.},
  Author                   = {Sueoka, N.},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1962},

  Month                    = {Apr},
  Pages                    = {582--592},
  Volume                   = {48},

  Keywords                 = {DNA, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {13918161},
  Timestamp                = {2012.09.26}
}

@Article{Sugase2007,
  Title                    = {Mechanism of coupled folding and binding of an intrinsically disordered protein},
  Author                   = {Sugase, Kenji and Dyson, H Jane and Wright, Peter E},
  Journal                  = {Nature},
  Year                     = {2007},
  Number                   = {7147},
  Pages                    = {1021--1025},
  Volume                   = {447},

  Owner                    = {ranjan},
  Publisher                = {Nature Publishing Group},
  Timestamp                = {2013.11.21}
}

@Article{Sugihara2012,
  Title                    = {Detecting Causality in Complex Ecosystems.},
  Author                   = {Sugihara, George and May, Robert and Ye, Hao and Hsieh, Chih-Hao and Deyle, Ethan and Fogarty, Michael and Munch, Stephan},
  Journal                  = {Science},
  Year                     = {2012},

  Month                    = {Sep},
  Number                   = {6106},
  Pages                    = {496-500},
  Volume                   = {338},

  Abstract                 = {Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. Here, we introduce a method, based on nonlinear state space reconstruction, that can distinguish causality from correlation. It extends to nonseparable weakly connected dynamic systems (cases not covered by the current Granger causality paradigm). The approach is illustrated both by simple models (where, in contrast to the real world, we know the underlying equations/relations and so can check the validity of our method) and by application to real ecological systems, including the controversial sardine-anchovy-temperature problem.},
  Institution              = {Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.},
  Medline-pst              = {aheadofprint},
  Owner                    = {ranjan},
  Pii                      = {science.1227079},
  Pmid                     = {22997134},
  Timestamp                = {2012.09.26}
}

@Article{Sugimoto2005,
  Title                    = {Systematic study of convex pentagonal tilings, I: Case of convex pentagons with four equal-length edges},
  Author                   = {Sugimoto, T. and Ogawa, T.},
  Journal                  = {Forma},
  Year                     = {2005},
  Pages                    = {1--18},
  Volume                   = {20},

  File                     = {Sugimoto2005.pdf:pdfs/Sugimoto2005.pdf:PDF}
}

@Article{Sugimoto2000,
  Title                    = {Tiling Problem of Convex Pentagon},
  Author                   = {Sugimoto, T. and Ogawa, T.},
  Journal                  = {Forma},
  Year                     = {2000},
  Pages                    = {75--79},
  Volume                   = {15},

  File                     = {Sugimoto2000.pdf:pdfs/Sugimoto2000.pdf:PDF}
}

@Article{Sui2007,
  Title                    = {Kinetics and equilibria of cis/trans isomerization of backbone amide bonds in peptoids.},
  Author                   = {Sui, Qiang and Borchardt, Dan and Rabenstein, Dallas L.},
  Journal                  = {J Am Chem Soc},
  Year                     = {2007},

  Month                    = {Oct},
  Number                   = {39},
  Pages                    = {12042--12048},
  Volume                   = {129},

  Abstract                 = {The biological activities of N-substituted glycine oligomers (peptoids) have been the subject of extensive research. As compared to peptides, both the cis and trans conformations of the backbone amide bonds of peptoids can be significantly populated. Thus, peptoids are mixtures of configurational isomers, with the number of isomers increasing by a factor of 2 with each additional monomer residue. Here we report the results of a study of the kinetics and equilibria of cis/trans isomerization of the amide bonds of N-acetylated peptoid monomers, dipeptoids, and tripeptoids by NMR spectroscopy. Resonance intensities indicate the cis conformation of the backbone amide bonds of the peptoids studied is more populated than is generally the case for the analogous secondary amide bond to proline residues in acyclic peptides. Rate constants were measured by inversion-magnetization transfer techniques over a range of temperatures, and activation parameters were derived from the temperature 
dependence of the rate constants. The rate of cis/trans isomerization by rotation around the amide bonds in the peptoids studied is generally slower than that around amide bonds to proline residues and takes place on the NMR inversion-magnetization transfer time scale only by rotation around the amide bond to the C-terminal peptoid residue.},
  Institution              = {Department of Chemistry, University of California, Riverside, California 92521, USA.},
  Keywords                 = {Amides, chemistry; Isomerism; Kinetics; Nuclear Magnetic Resonance, Biomolecular, methods; Peptoids, chemical synthesis/chemistry; Protein Conformation},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {17824612},
  Timestamp                = {2012.10.14}
}

@Article{Sun2016,
  author      = {Sun, Jing and Jiang, Xi and Lund, Reidar and Downing, Kenneth H. and Balsara, Nitash P. and Zuckermann, Ronald N.},
  title       = {Self-assembly of crystalline nanotubes from monodisperse amphiphilic diblock copolypeptoid tiles.},
  year        = {2016},
  volume      = {113},
  number      = {15},
  month       = {Apr},
  pages       = {3954--3959},
  abstract    = {The folding and assembly of sequence-defined polymers into precisely ordered nanostructures promises a class of well-defined biomimetic architectures with specific function. Amphiphilic diblock copolymers are known to self-assemble in water to form a variety of nanostructured morphologies including spheres, disks, cylinders, and vesicles. In all of these cases, the predominant driving force for assembly is the formation of a hydrophobic core that excludes water, whereas the hydrophilic blocks are solvated and extend into the aqueous phase. However, such polymer systems typically have broad molar mass distributions and lack the purity and sequence-defined structure often associated with biologically derived polymers. Here, we demonstrate that purified, monodisperse amphiphilic diblock copolypeptoids, with chemically distinct domains that are congruent in size and shape, can behave like molecular tile units that spontaneously assemble into hollow, crystalline nanotubes in water. The nanotubes consist of stacked, porous crystalline rings, and are held together primarily by side-chain van der Waals interactions. The peptoid nanotubes form without a central hydrophobic core, chirality, a hydrogen bond network, and electrostatic or π-π interactions. These results demonstrate the remarkable structure-directing influence of n-alkane and ethyleneoxy side chains in polymer self-assembly. More broadly, this work suggests that flexible, low-molecular-weight sequence-defined polymers can serve as molecular tile units that can assemble into precision supramolecular architectures.},
  institution = {Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; rnzuckermann@lbl.gov.},
  journal     = {Proc Natl Acad Sci U S A},
  medline-pst = {ppublish},
  owner       = {ranjan},
  pii         = {1517169113},
  pmid        = {27035944},
  timestamp   = {2016.09.01},
}

@Article{Sun2014,
  Title                    = {Crystallization in sequence-defined peptoid diblock copolymers induced by microphase separation},
  Author                   = {Sun, Jing and Teran, Alexander A and Liao, Xunxun and Balsara, Nitash P and Zuckermann, Ronald N},
  Journal                  = {Journal of the American Chemical Society},
  Year                     = {2014},
  Number                   = {5},
  Pages                    = {2070--2077},
  Volume                   = {136},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2015.06.15}
}

@Article{Sun2013,
  Title                    = {Peptoid polymers: a highly designable bioinspired material.},
  Author                   = {Sun, Jing and Zuckermann, Ronald N.},
  Journal                  = {ACS Nano},
  Year                     = {2013},

  Month                    = {Jun},
  Number                   = {6},
  Pages                    = {4715--4732},
  Volume                   = {7},

  Abstract                 = {Bioinspired polymeric materials are attracting increasing attention due to significant advantages over their natural counterparts: the ability to precisely tune their structures over a broad range of chemical and physical properties, increased stability, and improved processability. Polypeptoids, a promising class of bioinspired polymer based on a N-substituted glycine backbone, have a number of unique properties that bridge the material gap between proteins and bulk polymers. Peptoids combine the sequence specificity of biopolymers with the simpler intra/intermolecular interactions and robustness of traditional synthetic polymers. They are highly designable because hundreds of chemically diverse side chains can be introduced from simple building blocks. Peptoid polymers can be prepared by two distinct synthetic techniques offering access to two material subclasses: (1) automated solid-phase synthesis which enables precision sequence control and near absolute monodispersity up 
to chain lengths of ~50 monomers, and (2) a classical polymerization approach which allows access to higher molecular weights and larger-scale yields, but with less control over length and sequence. This combination of facile synthetic approaches makes polypeptoids a highly tunable, rapid polymer prototyping platform to investigate new materials that are intermediate between proteins and bulk polymers, in both their structure and their properties. In this paper, we review the methods to synthesize peptoid polymers and their applications in biomedicine and nanoscience, as both sequence-specific materials and as bulk polymers.},
  Doi                      = {10.1021/nn4015714},
  Institution              = {Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.},
  Keywords                 = {Biomimetic Materials, chemical synthesis/chemistry; Combinatorial Chemistry Techniques; Drug Design; Humans; Peptoids, chemical synthesis/chemistry; Polymerization},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {23721608},
  Timestamp                = {2014.04.28}
}

@Article{Syvanen1994,
  Title                    = {Horizontal gene transfer: evidence and possible consequences.},
  Author                   = {Syvanen, M.},
  Journal                  = {Annu Rev Genet},
  Year                     = {1994},
  Pages                    = {237--261},
  Volume                   = {28},

  Institution              = {Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis 95616.},
  Keywords                 = {Chromosomes, Bacterial; DNA Transposable Elements; Eukaryotic Cells, metabolism; Organelles, metabolism; Plants, genetics; Transformation, Genetic},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {7893125},
  Timestamp                = {2012.09.09}
}

@InProceedings{Szudzik2006,
  Title                    = {An elegant pairing function},
  Author                   = {Szudzik, Matthew},
  Booktitle                = {NKS2006 Conference},
  Year                     = {2006},

  Owner                    = {ranjan},
  Timestamp                = {2015.03.02}
}

@Article{Takada1999,
  Title                    = {Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer},
  Author                   = {Shoji Takada and Zaida Luthey-Schulten and Peter G. Wolynes},
  Journal                  = {J. Chem. Phys.},
  Year                     = {1999},
  Pages                    = {11616},
  Volume                   = {110},

  File                     = {:/home/ranjan/research/jabref/pdfs/Takada1999.pdf:PDF},
  Owner                    = {ranjan},
  Timestamp                = {2011.11.28}
}

@Article{Takagi2003,
  Title                    = {How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations.},
  Author                   = {Fumiko Takagi and Nobuyasu Koga and Shoji Takada},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2003},

  Month                    = {Sep},
  Number                   = {20},
  Pages                    = {11367--11372},
  Volume                   = {100},

  Abstract                 = {How the Escherichia coli GroEL/ES chaperonin assists folding of a substrate protein remains to be uncovered. Recently, it was suggested that confinement into the chaperonin cage itself can significantly accelerate folding of a substrate. Performing comprehensive molecular simulations of eight proteins confined into various sizes L of chaperonin-like cage, we explore how and to what extent protein thermodynamics and folding mechanisms are altered by the cage. We show that a substrate protein is remarkably stabilized by confinement; the estimated increase in denaturation temperature DeltaTf is as large as approximately 60 degrees C. For a protein of size R0, the stabilization DeltaTf scales as (R0/L)nu, where nu approximately 3, which is consistent with a mean field theory of polymer. We also found significant free energy cost of confining a protein, which increases with R0/L, indicating that the confinement requires external work provided by the chaperonin system. In kinetic 
study, we show the folding is accelerated in a modestly well confined case, which is consistent with a recent experimental result on ribulose-1,5-bisphosphate carboxylase-oxygenase folding and simulation results of a beta hairpin. Interestingly, the acceleration of folding is likely to be larger for a protein with more complex topology, as quantified by the contact order. We also show how ensemble of folding pathways are altered by the chaperonin-like cage calculating a variant of value used in the study of spontaneous folding.},
  Institution              = {PRESTO, Japan Science and Technology Corporation, and Department of Chemistry, Faculty of Science, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan.},
  Keywords                 = {Chaperonins, chemistry; Kinetics; Protein Folding; Proteins, chemistry; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {1831920100},
  Pmid                     = {12947041},
  Timestamp                = {2011.11.03}
}

@Article{Tama2005,
  Title                    = {Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis},
  Author                   = {Tama,F. and Brooks III,C.L.},
  Journal                  = JMB,
  Year                     = {2005},
  Number                   = {2},
  Pages                    = {299--314},
  Volume                   = {345},

  File                     = {Tama2005.pdf:pdfs/Tama2005.pdf:PDF}
}

@Article{Tama2002,
  Title                    = {The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus},
  Author                   = {Tama,F. and {Brooks III},C.L.},
  Journal                  = JMB,
  Year                     = {2002},
  Number                   = {3},
  Pages                    = {733--747},
  Volume                   = {318},

  File                     = {Tama2002.pdf:pdfs/Tama2002.pdf:PDF}
}

@Article{Tan2008,
  Title                    = {Genome-wide analysis of coding DNA and amino acid variation in Saccharomyces cerevisiae.},
  Author                   = {Haidong Tan and Jinxia Wang and Fan Yang and Zongbao K Zhao},
  Journal                  = {Yeast},
  Year                     = {2008},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {29--39},
  Volume                   = {25},

  Abstract                 = {The possible causes of variation on amino acid composition in the yeast Saccharomyces cerevisiae were investigated genome-wide. The results indicated that: (a) the base composition of coding DNA and amino acid composition was similar among all the chromosomes, which was in sharp contrast with the great varies of the composition of the individual's coding DNA and amino acid; (b) some amino acids (e.g. Cys and Trp) were not present in all the proteins; and (c) amino acid bias was associated with a base bias (in terms of A-, G-, C- and T-rich codons). Based on the third rule and a proposed universal trend of amino acid gain and loss in protein evolution, the changing pattern of coding DNA was predicted to be T- and C-accruing, whereas A and G were consistently reducing. All these results held the potential to reveal precisely how DNA ongoing change has a major effect on the composition of proteins.},
  Institution              = {Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian 116023, People's Republic of China. hdt@dicp.ac.cn},
  Keywords                 = {Amino Acids, genetics; Base Composition; DNA, Fungal, genetics; Evolution, Molecular; Genome, Fungal; Linear Models; Saccharomyces cerevisiae Proteins, genetics/metabolism; Saccharomyces cerevisiae, genetics/metabolism},
  Owner                    = {ranjan},
  Pmid                     = {17914746},
  Timestamp                = {2010.06.26}
}

@Article{Tang2006,
  Title                    = {The role of subunit hinges and molecular ``switches'' in the control of viral capsid polymorphism},
  Author                   = {Tang, J. and Johnson, J. M. and Dryden, K. A. and Young, M. J. and Zlotnick, A. and Johnson, J. E.},
  Journal                  = {J. Struct. Biol.},
  Year                     = {2006},
  Number                   = {1},
  Pages                    = {59--67},
  Volume                   = {154},

  File                     = {Tang2006.pdf:pdfs/Tang2006.pdf:PDF}
}

@Article{Tannenbaum2004b,
  Title                    = {Semiconservative replication in the quasispecies model.},
  Author                   = {Emmanuel Tannenbaum and Eric J Deeds and Eugene I Shakhnovich},
  Journal                  = {Phys Rev E Stat Nonlin Soft Matter Phys},
  Year                     = {2004},

  Month                    = {Jun},
  Number                   = {6 Pt 1},
  Pages                    = {061916},
  Volume                   = {69},

  Abstract                 = {This paper extends Eigen's quasispecies equations to account for the semiconservative nature of DNA replication. We solve the equations in the limit of infinite sequence length for the simplest case of a static, sharply peaked fitness landscape. We show that the error catastrophe occurs when micro, the product of sequence length and per base pair mismatch probability, exceeds 2 ln [2/ ( 1+1/k ) ], where k>1 is the first-order growth rate constant of the viable "master" sequence (with all other sequences having a first-order growth rate constant of 1 ). This is in contrast to the result of ln k for conservative replication. In particular, as k--> infinity, the error catastrophe is never reached for conservative replication, while for semiconservative replication the critical micro approaches 2 ln 2. Semiconservative replication is therefore considerably less robust than conservative replication to the effect of replication errors. We also show that the mean equilibrium fitness of 
a semiconservatively replicating system is given by k ( 2 e(-micro/2) -1 ) below the error catastrophe, in contrast to the standard result of k e(-micro) for conservative replication (derived by Kimura and Maruyama in 1966). From this result it is readily shown that semiconservative replication is necessary to account for the observation that, at sufficiently high mutagen concentrations, faster replicating cells will die more quickly than more slowly replicating cells. Thus, in contrast to Eigen's original model, the semiconservative quasispecies equations are able to provide a mathematical basis for explaining the efficacy of mutagens as chemotherapeutic agents.},
  Institution              = {Harvard University, Cambridge, Massachusetts 02138, USA. etannenb@fas.harvard.edu},
  Keywords                 = {Base Pair Mismatch; Base Sequence; Computer Simulation; DNA Damage, genetics; DNA Mutational Analysis, methods; DNA Repair, genetics; DNA Replication, genetics; Evolution, Molecular; Genetic Variation; Genetics, Population; Models, Genetic; Molecular Sequence Data; Mutation, genetics; Sequence Analysis, DNA, methods},
  Owner                    = {ranjan},
  Pmid                     = {15244626},
  Timestamp                = {2009.12.05}
}

@Article{Tannenbaum2004a,
  Title                    = {Solution of the quasispecies model for an arbitrary gene network.},
  Author                   = {Emmanuel Tannenbaum and Eugene I Shakhnovich},
  Journal                  = {Phys Rev E Stat Nonlin Soft Matter Phys},
  Year                     = {2004},

  Month                    = {Aug},
  Number                   = {2 Pt 1},
  Pages                    = {021903},
  Volume                   = {70},

  Abstract                 = {In this paper, we study the equilibrium behavior of Eigen's quasispecies equations for an arbitrary gene network. We consider a genome consisting of N genes, so that the full genome sequence sigma may be written as sigma= sigma1sigma2...sigmaN, where sigma(i) are sequences of individual genes. We assume a single fitness peak model for each gene, so that gene i has some "master" sequence sigma(i,0) for which it is functioning. The fitness landscape is then determined by which genes in the genome are functioning and which are not. The equilibrium behavior of this model may be solved in the limit of infinite sequence length. The central result is that, instead of a single error catastrophe, the model exhibits a series of localization to delocalization transitions, which we term an "error cascade." As the mutation rate is increased, the selective advantage for maintaining functional copies of certain genes in the network disappears, and the population distribution delocalizes over 
the corresponding sequence spaces. The network goes through a series of such transitions, as more and more genes become inactivated, until eventually delocalization occurs over the entire genome space, resulting in a final error catastrophe. This model provides a criterion for determining the conditions under which certain genes in a genome will lose functionality due to genetic drift. It also provides insight into the response of gene networks to mutagens. In particular, it suggests an approach for determining the relative importance of various genes to the fitness of an organism, in a more accurate manner than the standard "deletion set" method. The results in this paper also have implications for mutational robustness and what C.O. Wilke termed "survival of the flattest."},
  Institution              = {usetts 02138, USA. etannenb@fas.harvard.edu},
  Keywords                 = {Animals; Genetic Drift; Genetics; Genetics, Population; Models, Genetic; Models, Statistical; Models, Theoretical; Mutation; Species Specificity},
  Owner                    = {ranjan},
  Pmid                     = {15447511},
  Timestamp                = {2009.12.05}
}

@Article{Tannenbaum2004c,
  Title                    = {Error and repair catastrophes: A two-dimensional phase diagram in the quasispecies model.},
  Author                   = {Emmanuel Tannenbaum and Eugene I Shakhnovich},
  Journal                  = {Phys Rev E Stat Nonlin Soft Matter Phys},
  Year                     = {2004},

  Month                    = {Jan},
  Number                   = {1 Pt 1},
  Pages                    = {011902},
  Volume                   = {69},

  Abstract                 = {This paper develops a two-gene, single fitness peak model for determining the equilibrium distribution of genotypes in a unicellular population which is capable of genetic damage repair. The first gene, denoted by sigma(via), yields a viable organism with first-order growth rate constant k>1 if it is equal to some target "master" sequence sigma(via,0). The second gene, denoted by sigma(rep), yields an organism capable of genetic repair if it is equal to some target "master" sequence sigma(rep,0). This model is analytically solvable in the limit of infinite sequence length, and gives an equilibrium distribution which depends on micro identical with Lepsilon, the product of sequence length and per base pair replication error probability, and epsilon(r), the probability of repair failure per base pair. The equilibrium distribution is shown to exist in one of the three possible "phases." In the first phase, the population is localized about the viability and repairing master 
sequences. As epsilon(r) exceeds the fraction of deleterious mutations, the population undergoes a "repair" catastrophe, in which the equilibrium distribution is still localized about the viability master sequence, but is spread ergodically over the sequence subspace defined by the repair gene. Below the repair catastrophe, the distribution undergoes the error catastrophe when micro exceeds ln k/epsilon(r), while above the repair catastrophe, the distribution undergoes the error catastrophe when micro exceeds ln k/f(del), where f(del) denotes the fraction of deleterious mutations.},
  Institution              = {Harvard University, Cambridge, Massachusetts 02138, USA. etannenb@fas.harvard.edu},
  Keywords                 = {Computer Simulation; DNA Damage, genetics; DNA Mutational Analysis, methods; DNA Repair, genetics; Ecosystem; Evolution, Molecular; Genetic Variation; Models, Genetic; Mutation, genetics; Population Dynamics; Selection (Genetics)},
  Owner                    = {ranjan},
  Pmid                     = {14995642},
  Timestamp                = {2009.12.05}
}

@Article{Tannenbaum2005,
  Title                    = {Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms.},
  Author                   = {Emmanuel Tannenbaum and James L Sherley and Eugene I Shakhnovich},
  Journal                  = {Phys Rev E Stat Nonlin Soft Matter Phys},
  Year                     = {2005},

  Month                    = {Apr},
  Number                   = {4 Pt 1},
  Pages                    = {041914},
  Volume                   = {71},

  Abstract                 = {This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes of chromosome segregation: (1) random segregation, where the daughter chromosomes of a given parent chromosome segregate randomly into the stem cell and its differentiating sister cell and (2) "immortal DNA strand" co-segregation, for which the stem cell retains the daughter chromosomes with the oldest parent strands. Immortal strand co-segregation is a mechanism, originally proposed by [Cairns Nature (London) 255, 197 (1975)], by which stem cells preserve the integrity of their genomes. For random segregation, we develop an ordered strand pair formulation of the dynamics, analogous to the ordered strand pair formalism developed for quasispecies dynamics involving semiconservative replication with imperfect lesion repair (in this context, 
lesion repair is taken to mean repair of postreplication base-pair mismatches). Interestingly, a similar formulation is possible with immortal strand co-segregation, despite the fact that this segregation mechanism is age dependent. From our model we are able to mathematically show that, when lesion repair is imperfect, then immortal strand co-segregation leads to better preservation of the stem cell lineage than random chromosome segregation. Furthermore, our model allows us to estimate the optimal lesion repair efficiency for preserving an adult stem cell population for a given period of time. For human stem cells, we obtain that mispaired bases still present after replication and cell division should be left untouched, to avoid potentially fixing a mutation in both DNA strands.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA. etannenb@fas.harvard.edu},
  Keywords                 = {Adult; Cell Differentiation, genetics; Chromosome Mapping, methods; Chromosome Segregation, genetics; Computer Simulation; DNA Damage, genetics; DNA Mutational Analysis, methods; DNA Repair, genetics; DNA Replication, genetics; Evolution; Humans; Models, Genetic; Models, Statistical; Stem Cells, physiology},
  Owner                    = {ranjan},
  Pmid                     = {15903708},
  Timestamp                = {2009.12.05}
}

@Article{Tannenbaum2004,
  Title                    = {Imperfect DNA lesion repair in the semiconservative quasispecies model: derivation of the Hamming class equations and solution of the single-fitness peak landscape.},
  Author                   = {Emmanuel Tannenbaum and James L Sherley and Eugene I Shakhnovich},
  Journal                  = {Phys Rev E Stat Nonlin Soft Matter Phys},
  Year                     = {2004},

  Month                    = {Dec},
  Number                   = {6 Pt 1},
  Pages                    = {061915},
  Volume                   = {70},

  Abstract                 = {This paper develops a Hamming class formalism for the semiconservative quasispecies equations with imperfect lesion repair, first presented and analytically solved in Y. Brumer and E.I. Shakhnovich (q-bio.GN/0403018, 2004). Starting from the quasispecies dynamics over the space of genomes, we derive an equivalent dynamics over the space of ordered sequence pairs. From this set of equations, we are able to derive the infinite sequence length form of the dynamics for a class of fitness landscapes defined by a master genome. We use these equations to solve for a generalized single-fitness-peak landscape, where the master genome can sustain a maximum number of lesions and remain viable. We determine the mean equilibrium fitness and error threshold for this class of landscapes, and show that when lesion repair is imperfect, semiconservative replication displays characteristics from both conservative replication and semiconservative replication with perfect lesion repair. The work 
presented here provides a formulation of the model which greatly facilitates the analysis of a relatively broad class of fitness landscapes, and thus serves as a convenient springboard into biological applications of imperfect lesion repair.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA. etannenb@fas.harvard.edu},
  Keywords                 = {Animals; Base Pair Mismatch, genetics; Chromosome Mapping, methods; Computer Simulation; DNA Damage, genetics; DNA Mutational Analysis, methods; DNA Repair, genetics; DNA Replication, genetics; Evolution, Molecular; Genetic Variation, genetics; Genetics, Population; Humans; Models, Genetic; Selection (Genetics); Sequence Analysis, DNA, methods; Suppression, Genetic, genetics},
  Owner                    = {ranjan},
  Pmid                     = {15697410},
  Timestamp                = {2009.12.05}
}

@Article{Tatusov2000,
  Title                    = {The COG database: a tool for genome-scale analysis of protein functions and evolution.},
  Author                   = {R. L. Tatusov and M. Y. Galperin and D. A. Natale and E. V. Koonin},
  Journal                  = {Nucleic Acids Res},
  Year                     = {2000},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {33--36},
  Volume                   = {28},

  Abstract                 = {Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes (http://www. ncbi.nlm. nih.gov/COG). The COGs were constructed by applying the criterion of consistency of genome-specific best hits to the results of an exhaustive comparison of all protein sequences from these genomes. The database comprises 2091 COGs that include 56-83\% of the gene products from each of the complete bacterial and archaeal genomes and approximately 35\% of those from the yeast Saccharomyces cerevisiae genome. The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes.},
  Institution              = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.},
  Keywords                 = {Database Management Systems; Databases, Factual; Evolution, Molecular; Genome, Archaeal; Genome, Fungal; Internet; Phylogeny; Proteins, genetics/physiology},
  Owner                    = {ranjan},
  Pii                      = {gkd013},
  Pmid                     = {10592175},
  Timestamp                = {2011.05.11}
}

@Article{Tatusov1997,
  Title                    = {A genomic perspective on protein families.},
  Author                   = {R. L. Tatusov and E. V. Koonin and D. J. Lipman},
  Journal                  = {Science},
  Year                     = {1997},

  Month                    = {Oct},
  Number                   = {5338},
  Pages                    = {631--637},
  Volume                   = {278},

  Abstract                 = {In order to extract the maximum amount of information from the rapidly accumulating genome sequences, all conserved genes need to be classified according to their homologous relationships. Comparison of proteins encoded in seven complete genomes from five major phylogenetic lineages and elucidation of consistent patterns of sequence similarities allowed the delineation of 720 clusters of orthologous groups (COGs). Each COG consists of individual orthologous proteins or orthologous sets of paralogs from at least three lineages. Orthologs typically have the same function, allowing transfer of functional information from one member to an entire COG. This relation automatically yields a number of functional predictions for poorly characterized genomes. The COGs comprise a framework for functional and evolutionary genome analysis.},
  Institution              = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.},
  Keywords                 = {Amino Acid Sequence; Archaeal Proteins, chemistry/classification/genetics/physiology; Bacteria, chemistry/genetics; Bacterial Proteins, chemistry/classification/genetics/physiology; Conserved Sequence; Evolution, Molecular; Fungal Proteins, chemistry/classification/genetics/physiology; Genes, Archaeal; Genes, Bacterial; Genes, Fungal; Methanococcus, chemistry/genetics; Multigene Family; Phylogeny; Proteins, chemistry/classification/genetics/physiology; Saccharomyces cerevisiae, chemistry/genetics; Species Specificity},
  Owner                    = {ranjan},
  Pmid                     = {9381173},
  Timestamp                = {2011.04.21}
}

@Article{Tekaia1999,
  Title                    = {The genomic tree as revealed from whole proteome comparisons.},
  Author                   = {Tekaia, F. and Lazcano, A. and Dujon, B.},
  Journal                  = {Genome Res},
  Year                     = {1999},

  Month                    = {Jun},
  Number                   = {6},
  Pages                    = {550--557},
  Volume                   = {9},

  Abstract                 = {The availability of a number of complete cellular genome sequences allows the development of organisms' classification, taking into account their genome content, the loss or acquisition of genes, and overall gene similarities as signatures of common ancestry. On the basis of correspondence analysis and hierarchical classification methods, a methodological framework is introduced here for the classification of the available 20 completely sequenced genomes and partial information for Schizosaccharomyces pombe, Homo sapiens, and Mus musculus. The outcome of such an analysis leads to a classification of genomes that we call a genomic tree. Although these trees are phenograms, they carry with them strong phylogenetic signatures and are remarkably similar to 16S-like rRNA-based phylogenies. Our results suggest that duplication and deletion events that took place through evolutionary time were globally similar in related organisms. The genomic trees presented here place the Archaea in 
the proximity of the Bacteria when the whole gene content of each organism is considered, and when ancestral gene duplications are eliminated. Genomic trees represent an additional approach for the understanding of evolution at the genomic level and may contribute to the proper assessment of the evolutionary relationships between extant species.},
  Keywords                 = {Animals; Base Sequence; Evolution, Molecular; Genome; Genome, Human; Humans; Mice; Open Reading Frames, genetics; Schizosaccharomyces, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {10400922},
  Timestamp                = {2012.09.06}
}

@Article{Tekaia2006,
  Title                    = {Evolution of proteomes: fundamental signatures and global trends in amino acid compositions.},
  Author                   = {Fredj Tekaia and Edouard Yeramian},
  Journal                  = {BMC Genomics},
  Year                     = {2006},
  Pages                    = {307},
  Volume                   = {7},

  Abstract                 = {BACKGROUND: The evolutionary characterization of species and lifestyles at global levels is nowadays a subject of considerable interest, particularly with the availability of many complete genomes. Are there specific properties associated with lifestyles and phylogenies? What are the underlying evolutionary trends? One of the simplest analyses to address such questions concerns characterization of proteomes at the amino acids composition level. RESULTS: In this work, amino acid compositions of a large set of 208 proteomes, with significant number of representatives from the three phylogenetic domains and different lifestyles are analyzed, resorting to an appropriate multidimensional method: Correspondence analysis. The analysis reveals striking discrimination between eukaryotes, prokaryotic mesophiles and hyperthemophiles-themophiles, following amino acid usage. In sharp contrast, no similar discrimination is observed for psychrophiles. The observed distributional properties are 
compared with various inferred chronologies for the recruitment of amino acids into the genetic code. Such comparisons reveal correlations between the observed segregations of species following amino acid usage, and the separation of amino acids following early or late recruitment. CONCLUSION: A simple description of proteomes according to amino acid compositions reveals striking signatures, with sharp segregations or on the contrary non-discriminations following phylogenies and lifestyles. The distribution of species, following amino acid usage, exhibits a discrimination between [high GC]-[high optimal growth temperatures] and [low GC]-[moderate temperatures] characteristics. This discrimination appears to coincide closely with the separation of amino acids following their inferred early or late recruitment into the genetic code. Taken together the various results provide a consistent picture for the evolution of proteomes, in terms of amino acid usage.},
  Institution              = {Unit? de G?n?tique Mol?culaire des Levures (URA 2171 CNRS and UFR927 Univ, P,M, Curie), Institut Pasteur, 25, Rue du Dr Roux, 75724 Paris Cedex 15, France. tekaia@pasteur.fr},
  Keywords                 = {Amino Acids, analysis; Archaea, genetics/growth /&/ development; Bacteria, genetics/growth /&/ development; Base Composition; Eukaryotic Cells, chemistry; Evolution, Molecular; Genome; Phylogeny; Proteome, genetics; Species Specificity; Temperature},
  Owner                    = {ranjan},
  Pii                      = {1471-2164-7-307},
  Pmid                     = {17147802},
  Timestamp                = {2010.06.28}
}

@Article{Tekaia2006a,
  Title                    = {Evolution of proteomes: fundamental signatures and global trends in amino acid compositions.},
  Author                   = {Tekaia, Fredj and Yeramian, Edouard},
  Journal                  = {BMC Genomics},
  Year                     = {2006},
  Pages                    = {307},
  Volume                   = {7},

  Abstract                 = {The evolutionary characterization of species and lifestyles at global levels is nowadays a subject of considerable interest, particularly with the availability of many complete genomes. Are there specific properties associated with lifestyles and phylogenies? What are the underlying evolutionary trends? One of the simplest analyses to address such questions concerns characterization of proteomes at the amino acids composition level.In this work, amino acid compositions of a large set of 208 proteomes, with significant number of representatives from the three phylogenetic domains and different lifestyles are analyzed, resorting to an appropriate multidimensional method: Correspondence analysis. The analysis reveals striking discrimination between eukaryotes, prokaryotic mesophiles and hyperthemophiles-themophiles, following amino acid usage. In sharp contrast, no similar discrimination is observed for psychrophiles. The observed distributional properties are compared with various 
inferred chronologies for the recruitment of amino acids into the genetic code. Such comparisons reveal correlations between the observed segregations of species following amino acid usage, and the separation of amino acids following early or late recruitment.A simple description of proteomes according to amino acid compositions reveals striking signatures, with sharp segregations or on the contrary non-discriminations following phylogenies and lifestyles. The distribution of species, following amino acid usage, exhibits a discrimination between [high GC]-[high optimal growth temperatures] and [low GC]-[moderate temperatures] characteristics. This discrimination appears to coincide closely with the separation of amino acids following their inferred early or late recruitment into the genetic code. Taken together the various results provide a consistent picture for the evolution of proteomes, in terms of amino acid usage.},
  Keywords                 = {Amino Acids, analysis; Archaea, genetics/growth /&/ development; Bacteria, genetics/growth /&/ development; Base Composition; Eukaryotic Cells, chemistry; Evolution, Molecular; Genome; Phylogeny; Proteome, genetics; Species Specificity; Temperature},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {1471-2164-7-307},
  Pmid                     = {17147802},
  Timestamp                = {2012.09.26}
}

@Article{Templeton2008,
  Title                    = {The reality and importance of founder speciation in evolution.},
  Author                   = {Alan R Templeton},
  Journal                  = {Bioessays},
  Year                     = {2008},

  Month                    = {May},
  Number                   = {5},
  Pages                    = {470--479},
  Volume                   = {30},

  Abstract                 = {A founder event occurs when a new population is established from a small number of individuals drawn from a large ancestral population. Mayr proposed that genetic drift in an isolated founder population could alter the selective forces in an epistatic system, an observation supported by recent studies. Carson argued that a period of relaxed selection could occur when a founder population is in an open ecological niche, allowing rapid population growth after the founder event. Selectable genetic variation can actually increase during this founder-flush phase due to recombination, enhanced survival of advantageous mutations, and the conversion of non-additive genetic variance into additive variance in an epistatic system, another empirically confirmed prediction. Templeton combined the theories of Mayr and Carson with population genetic models to predict the conditions under which founder events can contribute to speciation, and these predictions are strongly confirmed by the 
empirical literature. Much of the criticism of founder speciation is based upon equating founder speciation to an adaptive peak shift opposed by selection. However, Mayr, Carson and Templeton all modeled a positive interaction of selection and drift, and Templeton showed that founder speciation is incompatible with peak-shift conditions. Although rare, founder speciation can have a disproportionate importance in adaptive innovation and radiation, and examples are given to show that "rare" does not mean "unimportant" in evolution. Founder speciation also interacts with other speciation mechanisms such that a speciation event is not a one-dimensional process due to either selection alone or drift alone.},
  Institution              = {Department of Biology, Washington University, St. Louis, Missouri 63130-4899, USA. temple_a@wustl.edu},
  Keywords                 = {Animals; Apolipoproteins E, genetics; Biological Evolution; Drosophila, genetics; Epistasis, Genetic; Female; Founder Effect; Genetic Drift; Genetic Speciation; Genetic Variation; Genetics, Population; Humans; Male; Models, Genetic; Phenotype; Receptors, LDL, genetics; Selection, Genetic},
  Owner                    = {ranjan},
  Pmid                     = {18404703},
  Timestamp                = {2011.04.28}
}

@Article{Teng2007,
  Title                    = {Immunoglobulin somatic hypermutation},
  Author                   = {Teng, Grace and Papavasiliou, F Nina},
  Journal                  = {Annu. Rev. Genet.},
  Year                     = {2007},
  Pages                    = {107--120},
  Volume                   = {41},

  Owner                    = {ranjan},
  Publisher                = {Annual Reviews},
  Timestamp                = {2013.12.03}
}

@Article{Teschke1993,
  Title                    = {Inhibition of viral capsid assembly by 1,1'-bi(4-anilinonaphthalene-5-sulfonic acid).},
  Author                   = {Teschke, C.M. and King, J. and Prevelige Jr., P. E.},
  Journal                  = {Biochemistry},
  Year                     = {1993},
  Number                   = {40},
  Pages                    = {10658--10665},
  Volume                   = {32}
}

@Article{Thirumalai2003,
  Title                    = {Caging helps proteins fold.},
  Author                   = {D. Thirumalai and Dmitri K Klimov and George H Lorimer},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2003},

  Month                    = {Sep},
  Number                   = {20},
  Pages                    = {11195--11197},
  Volume                   = {100},

  Institution              = {Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA. thirum@glue.umd.edu},
  Keywords                 = {Protein Conformation; Protein Folding},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {2035072100},
  Pmid                     = {14506295},
  Timestamp                = {2011.11.03}
}

@Article{Thomas2002,
  Title                    = {Aromatic side-chain interactions in proteins. I. Main structural features},
  Author                   = {Thomas, Annick and Meurisse, Rita and Charloteaux, Benoit and Brasseur, Robert},
  Journal                  = {Proteins: Structure, Function, and Bioinformatics},
  Year                     = {2002},
  Number                   = {4},
  Pages                    = {628--634},
  Volume                   = {48},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2013.11.30}
}

@Article{Thomas2005,
  Title                    = {Mechanisms of, and barriers to, horizontal gene transfer between bacteria.},
  Author                   = {Thomas, Christopher M. and Nielsen, Kaare M.},
  Journal                  = {Nat Rev Microbiol},
  Year                     = {2005},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {711--721},
  Volume                   = {3},

  Abstract                 = {Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent. Transformation involves the release of naked DNA followed by uptake and recombination. Homologous recombination and DNA-repair processes normally limit this to DNA from similar bacteria. However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition.},
  Institution              = {School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK. c.m.thomas@bham.ac.uk},
  Keywords                 = {Bacteria, genetics; Conjugation, Genetic, genetics; Evolution, Molecular; Gene Transfer Techniques; Models, Genetic; Mutation; Transformation, Bacterial, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nrmicro1234},
  Pmid                     = {16138099},
  Timestamp                = {2012.09.10}
}

@Book{Thompson1992,
  Title                    = {On Growth and Form. Dover reprint of 1942 2nd ed. (1st ed., 1917).},
  Author                   = {Thompson,D.W.},
  Editor                   = {Bonner,J.T.},
  Publisher                = {Cambridge University Press},
  Year                     = {1992}
}

@Article{Thornton1999,
  Title                    = {Protein folds, functions and evolution.},
  Author                   = {J. M. Thornton and C. A. Orengo and A. E. Todd and F. M. Pearl},
  Journal                  = {J Mol Biol},
  Year                     = {1999},

  Month                    = {Oct},
  Number                   = {2},
  Pages                    = {333--342},
  Volume                   = {293},

  Abstract                 = {The evolution of proteins and their functions is reviewed from a structural perspective in the light of the current database. Protein domain families segregate unequally between the three major classes, the 32 different architectures and almost 700 folds observed to date. We find that the number of new topologies is still increasing, although 25 new structures are now determined for each new topology. The corresponding analysis and classification of function is only just beginning, fuelled by the genome data. The structural data revealed unexpected conservations and divergence of function both within and between families. The next five years will see the compilation of a definitive dictionary of protein families and their related functions, based on structural data which reveals relationships hidden at the sequence level. Such information will provide the foundation to build a better understanding of the molecular basis of biological complexity and hopefully to facilitate 
rational molecular design.},
  File                     = {Thornton1999.pdf:pdfs/Thornton1999.pdf:PDF},
  Institution              = {Biochemistry and Molecular Biology Department, University College London, University of London, Gower Street, London, WC1E 6BT, UK. thornton@biochem.ucl.ac.uk},
  Keywords                 = {Animals; Databases, Factual; Enzymes, chemistry/classification/metabolism; Evolution, Molecular; Genome; Humans; Phylogeny; Protein Folding; Protein Structure, Secondary; Proteins, chemistry/classification/metabolism; Structure-Activity Relationship},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(99)93054-1},
  Pmid                     = {10529349},
  Timestamp                = {2009.09.14}
}

@Article{Thornton2001,
  Title                    = {Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions.},
  Author                   = {J. W. Thornton},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2001},

  Month                    = {May},
  Number                   = {10},
  Pages                    = {5671--5676},
  Volume                   = {98},

  Abstract                 = {The evolution of novelty in tightly integrated biological systems, such as hormones and their receptors, seems to challenge the theory of natural selection: it has not been clear how a new function for any one part (such as a ligand) can be selected for unless the other members of the system (e.g., a receptor) are already present. Here I show-based on identification and phylogenetic analysis of steroid receptors in basal vertebrates and reconstruction of the sequences and functional attributes of ancestral proteins-that the first steroid receptor was an estrogen receptor, followed by a progesterone receptor. Genome mapping and phylogenetic analyses indicate that the full complement of mammalian steroid receptors evolved from these ancient receptors by two large-scale genome expansions, one before the advent of jawed vertebrates and one after. Specific regulation of physiological processes by androgens and corticoids are relatively recent innovations that emerged after these 
duplications. These findings support a model of ligand exploitation in which the terminal ligand in a biosynthetic pathway is the first for which a receptor evolves; selection for this hormone also selects for the synthesis of intermediates despite the absence of receptors, and duplicated receptors then evolve affinity for these substances. In this way, novel hormone-receptor pairs are created, and an integrated system of increasing complexity elaborated. This model suggests that ligands for some "orphan" receptors may be found among intermediates in the synthesis of ligands for phylogenetically related receptors.},
  Institution              = {The Earth Institute and Department of Biological Sciences, Columbia University, M.C. 2430, New York, NY 10027, USA. jt121@columbia.edu},
  Keywords                 = {Animals; Evolution, Molecular; Lampreys, genetics; Ligands; Molecular Sequence Data; Phylogeny; Receptors, Estrogen, genetics/metabolism; Receptors, Steroid, genetics/metabolism},
  Owner                    = {ranjan},
  Pii                      = {091553298},
  Pmid                     = {11331759},
  Timestamp                = {2010.04.20}
}

@Article{Thorpe2007,
  Title                    = {Molecular evolution of affinity and flexibility in the immune system.},
  Author                   = {Ian F Thorpe and Charles L {Brooks III}},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2007},

  Month                    = {May},
  Number                   = {21},
  Pages                    = {8821--8826},
  Volume                   = {104},

  Abstract                 = {The immune system responds to the introduction of foreign antigens by rapidly evolving antibodies with increasing affinity for the antigen (i.e., maturation). To investigate the factors that control this process at the molecular level, we have assessed the changes in flexibility that accompany ligand binding at four stages of maturation in the 4-4-20 antibody. Our studies, based on molecular dynamics, indicate that increased affinity for the target ligand is associated with a decreased entropic cost to binding. The entropy of binding is unfavorable, opposing favorable enthalpic contributions that arise during complex formation. Computed binding free energies for the various antibody-ligand complexes qualitatively reproduce the trends observed in the experimentally derived values, although the absolute magnitude of free-energy differences is overestimated. Our results support the existence of a correlation between high-affinity interactions and decreased protein flexibility in 
this series of antibody molecules. This observation is likely to be a general feature of molecular association processes and key to the molecular evolution of antibody responses.},
  Institution              = {Center for Theoretical Biological Physics and Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.},
  Keywords                 = {Antibodies, chemistry/genetics/immunology; Antigens, chemistry/genetics/immunology; Computer Simulation; Crystallography, X-Ray; Evolution, Molecular; Immune System, chemistry/immunology/metabolism; Protein Binding; Protein Processing, Post-Translational; Protein Structure, Quaternary; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {0610064104},
  Pmid                     = {17488816},
  Timestamp                = {2009.12.05}
}

@Article{Thuman1998,
  Title                    = {Role of the scaffolding protein in P22 procapsid size determination suggested by T = 4 and T = 7 procapsid structures.},
  Author                   = {Thuman-Commike,P.A. and Greene, B. and Malinski, J.A. and King, J. and Chiu, W.},
  Journal                  = {Biophys J.},
  Year                     = {1998},
  Number                   = {1},
  Pages                    = {559--568},
  Volume                   = {74},

  File                     = {Thuman1998.pdf:pdfs/Thuman1998.pdf:PDF}
}

@Article{Tiana2000,
  Title                    = {Hiking in the energy landscape in sequence space: a bumpy road to good folders.},
  Author                   = {G. Tiana and R. A. Broglia and E. I. Shakhnovich},
  Journal                  = {Proteins},
  Year                     = {2000},

  Month                    = {May},
  Number                   = {3},
  Pages                    = {244--251},
  Volume                   = {39},

  Abstract                 = {With the help of a simple 20-letter lattice model of heteropolymers, we investigated the energy landscape in the space of designed good-folder sequences. Low-energy sequences form clusters, interconnected via neutral networks, in the space of sequences. Residues that play a key role in the foldability of the chain and in the stability of the native state are highly conserved, even among the chains belonging to different clusters. If, according to the interaction matrix, some strong attractive interactions are almost degenerate (i.e., they can be realized by more than one type of amino acid contacts), sequence clusters group into a few superclusters. Sequences belonging to different superclusters are dissimilar, displaying very small ( approximately 10\%) similarity, and residues in key sites are, as a rule, not conserved. Similar behavior is observed in the analysis of real protein sequences.},
  Institution              = {The Niels Bohr Institute, University of Copenhagen, Copenaghen, Denmark.},
  Keywords                 = {Amino Acid Sequence; Evolution, Molecular; Models, Chemical; Models, Molecular; Monte Carlo Method; Peptides, chemistry; Protein Conformation; Protein Folding},
  Owner                    = {ranjan},
  Pii                      = {3.0.CO;2-#},
  Pmid                     = {10737946},
  Timestamp                = {2009.12.05}
}

@Article{Tiana2004a,
  Title                    = {The evolution dynamics of model proteins.},
  Author                   = {Guido Tiana and Nikolay V Dokholyan and Ricardo A Broglia and Eugene I Shakhnovich},
  Journal                  = {J Chem Phys},
  Year                     = {2004},

  Month                    = {Aug},
  Number                   = {5},
  Pages                    = {2381--2389},
  Volume                   = {121},

  Abstract                 = {Explicit simulations of protein evolution, where protein chains are described at a molecular, although simplified, level provide important information to understand the similarities found to exist between known proteins. The results of such simulations suggest that a number of evolutionary-related quantities, such as the distribution of sequence similarity for structurally similar proteins, are controlled by evolutionary kinetics and do not reflect an equilibrium state. An important result for phylogeny is that a subset of the residues of each protein evolve on a much larger time scale than the other residues.},
  Institution              = {Department of Physics, University of Milano, via Celoria 16, 20133, Italy.},
  Owner                    = {ranjan},
  Pmid                     = {15260793},
  Timestamp                = {2009.12.05}
}

@Article{Tiana2004,
  Title                    = {Imprint of evolution on protein structures.},
  Author                   = {Guido Tiana and Boris E Shakhnovich and Nikolay V Dokholyan and Eugene I Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2004},

  Month                    = {Mar},
  Number                   = {9},
  Pages                    = {2846--2851},
  Volume                   = {101},

  Abstract                 = {We attempt to understand the evolutionary origin of protein folds by simulating their divergent evolution with a three-dimensional lattice model. Starting from an initial seed lattice structure, evolution of model proteins progresses by sequence duplication and subsequent point mutations. A new gene's ability to fold into a stable and unique structure is tested each time through direct kinetic folding simulations. Where possible, the algorithm accepts the new sequence and structure and thus a "new protein structure" is born. During the course of each run, this model evolutionary algorithm provides several thousand new proteins with diverse structures. Analysis of evolved structures shows that later evolved structures are more designable than seed structures as judged by recently developed structural determinant of protein designability, as well as direct estimate of designability for selected structures by thermodynamic sampling of their sequence space. We test the significance 
of this trend predicted on lattice models on real proteins and show that protein domains that are found in eukaryotic organisms only feature statistically significant higher designability than their prokaryotic counterparts. These results present a fundamental view on protein evolution highlighting the relative roles of structural selection and evolutionary dynamics on genesis of modern proteins.},
  File                     = {Tiana2004.pdf:pdfs/Tiana2004.pdf:PDF},
  Institution              = {Department of Physics and Istituto Nazionale di Fisica Nucleare, University of Milano, Via Celoria 16, 20133 Milan, Italy.},
  Keywords                 = {Algorithms; Evolution, Molecular; Models, Biological; Proteins, chemistry; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {0306638101},
  Pmid                     = {14970345},
  Timestamp                = {2009.12.05}
}

@Article{Tice2004,
  Title                    = {Photosynthetic microbial mats in the 3,416-Myr-old ocean.},
  Author                   = {Michael M Tice and Donald R Lowe},
  Journal                  = {Nature},
  Year                     = {2004},

  Month                    = {Sep},
  Number                   = {7008},
  Pages                    = {549--552},
  Volume                   = {431},

  Abstract                 = {Recent re-evaluations of the geological record of the earliest life on Earth have led to the suggestion that some of the oldest putative microfossils and carbonaceous matter were formed through abiotic hydrothermal processes. Similarly, many early Archaean (more than 3,400-Myr-old) cherts have been reinterpreted as hydrothermal deposits rather than products of normal marine sedimentary processes. Here we present the results of a field, petrographic and geochemical study testing these hypotheses for the 3,416-Myr-old Buck Reef Chert, South Africa. From sedimentary structures and distributions of sand and mud, we infer that deposition occurred in normal open shallow to deep marine environments. The siderite enrichment that we observe in deep-water sediments is consistent with a stratified early ocean. We show that most carbonaceous matter was formed by photosynthetic mats within the euphotic zone and distributed as detrital matter by waves and currents to surrounding environments. 
We find no evidence that hydrothermal processes had any direct role in the deposition of either the carbonaceous matter or the enclosing sediments. Instead, we conclude that photosynthetic organisms had evolved and were living in a stratified ocean supersaturated in dissolved silica 3,416 Myr ago.},
  Institution              = {Department of Geological and Environmental Sciences, Stanford University, Stanford, California 94305, USA. mtice@pangea.stanford.edu},
  Keywords                 = {Animals; Anthozoa; Biofilms; Biogenesis; Carbon, metabolism; Evolution; Fossils; Geologic Sediments, chemistry/microbiology; Models, Biological; Oceans and Seas; Photosynthesis; Silicon Dioxide, chemistry/metabolism; South Africa; Temperature; Time Factors; Water Movements},
  Owner                    = {ranjan},
  Pii                      = {nature02888},
  Pmid                     = {15457255},
  Timestamp                = {2010.11.07}
}

@Article{Tiessen2012,
  Title                    = {Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes.},
  Author                   = {Tiessen, Axel and P{\'{e}}rez-Rodr{\'{\i}}guez, Paulino and Delaye-Arredondo, Luis Jos{\'{e}}},
  Journal                  = {BMC Res Notes},
  Year                     = {2012},
  Pages                    = {85},
  Volume                   = {5},

  Abstract                 = {The sizes of proteins are relevant to their biochemical structure and for their biological function. The statistical distribution of protein lengths across a diverse set of taxa can provide hints about the evolution of proteomes.Using the full genomic sequences of over 1,302 prokaryotic and 140 eukaryotic species two datasets containing 1.2 and 6.1 million proteins were generated and analyzed statistically. The lengthwise distribution of proteins can be roughly described with a gamma type or log-normal model, depending on the species. However the shape parameter of the gamma model has not a fixed value of 2, as previously suggested, but varies between 1.5 and 3 in different species. A gamma model with unrestricted shape parameter described best the distributions in ~48\% of the species, whereas the log-normal distribution described better the observed protein sizes in 42\% of the species. The gamma restricted function and the sum of exponentials distribution had a better fitting 
in only ~5\% of the species. Eukaryotic proteins have an average size of 472 aa, whereas bacterial (320 aa) and archaeal (283 aa) proteins are significantly smaller (33-40\% on average). Average protein sizes in different phylogenetic groups were: Alveolata (628 aa), Amoebozoa (533 aa), Fornicata (543 aa), Placozoa (453 aa), Eumetazoa (486 aa), Fungi (487 aa), Stramenopila (486 aa), Viridiplantae (392 aa). Amino acid composition is biased according to protein size. Protein length correlated negatively with \%C, \%M, \%K, \%F, \%R, \%W, \%Y and positively with \%D, \%E, \%Q, \%S and \%T. Prokaryotic proteins had a different protein size bias for \%E, \%G, \%K and \%M as compared to eukaryotes.Mathematical modeling of protein length empirical distributions can be used to asses the quality of small ORFs annotation in genomic releases (detection of too many false positive small ORFs). There is a negative correlation between average protein size and total number of proteins among eukaryotes but not in prokaryotes.
 The \%GC content is positively correlated to total protein number and protein size in prokaryotes but not in eukaryotes. Small proteins have a different amino acid bias than larger proteins. Compared to prokaryotic species, the evolution of eukaryotic proteomes was characterized by increased protein number (massive gene duplication) and substantial changes of protein size (domain addition/subtraction).},
  Doi                      = {10.1186/1756-0500-5-85},
  Institution              = {Departamento de Ingeniería Genética, CINVESTAV Irapuato, Irapuato, CP 36821, Mexico. atiessen@ira.cinvestav.mx.},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {1756-0500-5-85},
  Pmid                     = {22296664},
  Timestamp                = {2014.02.24}
}

@Article{Todd2001,
  Title                    = {Evolution of function in protein superfamilies, from a structural perspective.},
  Author                   = {A. E. Todd and C. A. Orengo and J. M. Thornton},
  Journal                  = {J Mol Biol},
  Year                     = {2001},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {1113--1143},
  Volume                   = {307},

  Abstract                 = {The recent growth in protein databases has revealed the functional diversity of many protein superfamilies. We have assessed the functional variation of homologous enzyme superfamilies containing two or more enzymes, as defined by the CATH protein structure classification, by way of the Enzyme Commission (EC) scheme. Combining sequence and structure information to identify relatives, the majority of superfamilies display variation in enzyme function, with 25 \% of superfamilies in the PDB having members of different enzyme types. We determined the extent of functional similarity at different levels of sequence identity for 486,000 homologous pairs (enzyme/enzyme and enzyme/non-enzyme), with structural and sequence relatives included. For single and multi-domain proteins, variation in EC number is rare above 40 \% sequence identity, and above 30 \%, the first three digits may be predicted with an accuracy of at least 90 \%. For more distantly related proteins sharing less than 30 
\% sequence identity, functional variation is significant, and below this threshold, structural data are essential for understanding the molecular basis of observed functional differences. To explore the mechanisms for generating functional diversity during evolution, we have studied in detail 31 diverse structural enzyme superfamilies for which structural data are available. A large number of variations and peculiarities are observed, at the atomic level through to gross structural rearrangements. Almost all superfamilies exhibit functional diversity generated by local sequence variation and domain shuffling. Commonly, substrate specificity is diverse across a superfamily, whilst the reaction chemistry is maintained. In many superfamilies, the position of catalytic residues may vary despite playing equivalent functional roles in related proteins. The implications of functional diversity within supefamilies for the structural genomics projects are discussed. More detailed information on these superfamilies 
is available at http://www.biochem.ucl.ac.uk/bsm/FAM-EC/.},
  File                     = {Todd2001.pdf:pdfs/Todd2001.pdf:PDF},
  Institution              = {Biochemistry and Molecular Biology Department, University College London, Gower Street, London, WC1E 6BT, UK.},
  Keywords                 = {Binding Sites; Catalysis; Conserved Sequence; Databases as Topic; Enzymes, chemistry/classification/metabolism; Evolution, Molecular; Metals, metabolism; Models, Molecular; Multigene Family; Mutation; Protein Binding; Protein Structure, Quaternary; Protein Structure, Tertiary; Protein Subunits; Proteins, chemistry/classification/metabolism; Repetitive Sequences, Amino Acid; Sequence Homology, Amino Acid; Structure-Activity Relationship; Substrate Specificity},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(01)94513-9},
  Pmid                     = {11286560},
  Timestamp                = {2009.09.14}
}

@Article{Todd1999,
  Title                    = {Evolution of protein function, from a structural perspective.},
  Author                   = {A. E. Todd and C. A. Orengo and J. M. Thornton},
  Journal                  = {Curr Opin Chem Biol},
  Year                     = {1999},

  Month                    = {Oct},
  Number                   = {5},
  Pages                    = {548--556},
  Volume                   = {3},

  Abstract                 = {The recent growth in structural data, and ensuing analyses, have revealed the structural and functional versatility of protein families. With respect to enzymes, local active-site mutations, variations in surface loops and recruitment of additional domains accommodate the diverse substrate specificities and catalytic activities observed within several superfamilies. Conversely, some functions have more than one structural solution, having evolved independently several times during evolution. Combined with the existence of multi-functional genes, which have arisen by gene recruitment, these phenomena must be considered in the process of genome annotation.},
  Institution              = {Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology, University College London, Gower Street, London,WC1E 6BT, UK.},
  Keywords                 = {Animals; Catalysis; Enzymes, genetics/physiology; Evolution, Molecular; Humans; Protein Folding; Structure-Activity Relationship; Substrate Specificity},
  Owner                    = {ranjan},
  Pii                      = {S1367-5931(99)00007-1},
  Pmid                     = {10508675},
  Timestamp                = {2009.09.14}
}

@Article{Tokuriki2009,
  Title                    = {Protein dynamism and evolvability.},
  Author                   = {Nobuhiko Tokuriki and Dan S Tawfik},
  Journal                  = {Science},
  Year                     = {2009},

  Month                    = {Apr},
  Number                   = {5924},
  Pages                    = {203--207},
  Volume                   = {324},

  Abstract                 = {The traditional view that proteins possess absolute functional specificity and a single, fixed structure conflicts with their marked ability to adapt and evolve new functions and structures. We consider an alternative, "avant-garde view" in which proteins are conformationally dynamic and exhibit functional promiscuity. We surmise that these properties are the foundation stones of protein evolvability; they facilitate the divergence of new functions within existing folds and the evolution of entirely new folds. Packing modes of proteins also affect their evolvability, and poorly packed, disordered, and conformationally diverse proteins may exhibit high evolvability. This dynamic view of protein structure, function, and evolvability is extrapolated to describe hypothetical scenarios for the evolution of the early proteins and future research directions in the area of protein dynamism and evolution.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Tokuriki2009.pdf:PDF},
  Institution              = {Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.},
  Keywords                 = {Catalytic Domain; Evolution, Molecular; Ligands; Models, Molecular; Mutation; Protein Conformation; Protein Folding; Proteins, chemistry/genetics/physiology},
  Owner                    = {ranjan},
  Pii                      = {324/5924/203},
  Pmid                     = {19359577},
  Timestamp                = {2010.02.09}
}

@Article{Tompa2011,
  Title                    = {Unstructural biology coming of age.},
  Author                   = {Tompa, Peter},
  Journal                  = {Curr Opin Struct Biol},
  Year                     = {2011},

  Month                    = {Jun},
  Number                   = {3},
  Pages                    = {419--425},
  Volume                   = {21},

  Abstract                 = {It is now generally accepted that many proteins or protein domains (intrinsically disordered proteins, IDPs) lack a well-defined tertiary structure under functional conditions. Due to recent concerted activity, a critical transition in this field is gaining momentum, in which qualitative observations are turned into quantitative structural models of IDPs. Here, it is suggested that the transition is set up by the synergy of: (i) more advanced bioinformatic tools for the prediction of disorder and function of IDPs, (ii) ensemble description of their structure and dynamics in both free and bound states, down to the single molecule level, (iii) advent of in-cell approaches for characterizing their structure and function in vivo, and (iv) generation of small-molecule inhibitors both against their binding partners and IDPs themselves. In all, we suggest that due to steady advance in these areas, the field of 'unstructural' biology is rapidly maturing to a state where it can provide 
quantitative models of proteins functioning without well-defined three-dimensional structures.},
  Doi                      = {10.1016/j.sbi.2011.03.012},
  Institution              = {Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary. tompa@enzim.hu},
  Keywords                 = {Animals; Computational Biology; Drug Design; Evolution, Molecular; Humans; Protein Binding; Protein Conformation; Protein Folding; Protein Interaction Domains and Motifs; Proteins, chemistry/genetics/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0959-440X(11)00064-9},
  Pmid                     = {21514142},
  Timestamp                = {2013.12.14}
}

@Article{Tompa2005a,
  Title                    = {The interplay between structure and function in intrinsically unstructured proteins.},
  Author                   = {Tompa, Peter},
  Journal                  = {FEBS Lett},
  Year                     = {2005},

  Month                    = {Jun},
  Number                   = {15},
  Pages                    = {3346--3354},
  Volume                   = {579},

  Abstract                 = {Intrinsically unstructured proteins (IUPs) are common in various proteomes and occupy a unique structural and functional niche in which function is directly linked to structural disorder. The evidence that these proteins exist without a well-defined folded structure in vitro is compelling, and justifies considering them a separate class within the protein world. In this paper, novel advances in the rapidly advancing field of IUPs are reviewed, with the major attention directed to the evidence of their unfolded character in vivo, the interplay of their residual structure and their various functional modes and the functional benefits their malleable structural state provides. Via all these details, it is demonstrated that in only a couple of years after its conception, the idea of protein disorder has already come of age and transformed our basic concepts of protein structure and function.},
  Doi                      = {10.1016/j.febslet.2005.03.072},
  Institution              = {Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary. tompa@enzim.hu},
  Keywords                 = {Animals; Protein Conformation; Protein Folding; Proteins, chemistry/classification/metabolism; Structure-Activity Relationship},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0014-5793(05)00424-2},
  Pmid                     = {15943980},
  Timestamp                = {2013.12.08}
}

@Article{Tompa2008,
  Title                    = {Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions.},
  Author                   = {Tompa, Peter and Fuxreiter, Monika},
  Journal                  = {Trends Biochem Sci},
  Year                     = {2008},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {2--8},
  Volume                   = {33},

  Abstract                 = {The notion that all protein functions are determined through macromolecular interactions is the driving force behind current efforts that aim to solve the structures of all cellular complexes. Recent findings, however, demonstrate a significant amount of structural disorder or polymorphism in protein complexes, a phenomenon that has been largely overlooked thus far. It is our view that such disorder can be classified into four mechanistic categories, covering a continuous spectrum of structural states from static to dynamic disorder and from segmental to full disorder. To emphasize its generality and importance, we suggest a generic term, 'fuzziness', for this phenomenon. Given the crucial role of protein disorder in protein-protein interactions and in regulatory processes, we envision that fuzziness will become integral to understanding the interactome.},
  Doi                      = {10.1016/j.tibs.2007.10.003},
  Institution              = {Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary. tompa@enzim.hu},
  Keywords                 = {Models, Molecular; Polymorphism, Genetic; Protein Binding; Protein Conformation; Protein Interaction Mapping; Protein Structure, Tertiary; Proteins, chemistry/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0968-0004(07)00285-X},
  Pmid                     = {18054235},
  Timestamp                = {2013.12.14}
}

@Article{Torres1996,
  Title                    = {Competing research programmes on the origin of life},
  Author                   = {Juan Manuel Torres},
  Journal                  = {Journal for General Philosophy of Science},
  Year                     = {1996},
  Pages                    = {325-346},
  Volume                   = {27},

  Owner                    = {ranjan},
  Timestamp                = {2012.04.05}
}

@Article{Torshin2001,
  Title                    = {Clustering amino acid contents of protein domains: biochemical functions of proteins and implications for origin of biological macromolecules.},
  Author                   = {I. Y. Torshin},
  Journal                  = {Front Biosci},
  Year                     = {2001},

  Month                    = {Apr},
  Pages                    = {A1--A12},
  Volume                   = {6},

  Abstract                 = {Structural classes of protein domains correlate with their amino acid compositions. Several successful algorithms (that use only amino acid composition) have been elaborated for the prediction of structural class or potential biochemical significance. This work deals with dynamic classification (clustering) of the domains on the basis of their amino acid composition. Amino acid contents of domains from a non-redundant PDB set were clustered in 20-dimensional space of amino acid contents. Despite the variations of an empirical parameter and non-redundancy of the set, only one large cluster (tens-hundreds of proteins) surrounded by hundreds of small clusters (1-5 proteins), was identified. The core of the largest cluster contains at least 64\% DNA (nucleotide)-interacting protein domains from various sources. About 90\% of the proteins of the core are intracellular proteins. 83\% of the DNA/nucleotide interacting domains in the core belong to the mixed alpha-beta folds (a+b, a/b), 
14\% are all-alpha (mostly helices) and all-beta (mostly beta-strands) proteins. At the same time, when core domains that belong to one organism (E.coli) are considered, over 80\% of them prove to be DNA/nucleotide interacting proteins. The core is compact: amino acid contents of domains from the core lie in relatively narrow and specific ranges. The core also contains several Fe-S cluster-binding domains, amino acid contents of the core overlap with ferredoxin and CO-dehydrogenase clusters, the oldest known proteins. As Fe-S clusters are thought to be the first biocatalysts, the results are discussed in relation to contemporary experiments and models dealing with the origin of biological macromolecules. The origin of most primordial proteins is considered here to be a result of co-adsorption of nucleotides and amino acids on specific clays, followed by en-block polymerization of the adsorbed mixtures of amino acids.},
  File                     = {Torshin2001.pdf:pdfs/Torshin2001.pdf:PDF},
  Institution              = {Laboratory Of Chemical Kinetics And Catalysis, Chem. Dept. of Moscow State University, Moscow, 119899, Russia. biotiy@hydra.cs.gsu.edu},
  Keywords                 = {Aluminum Silicates, chemistry; Amino Acids, biosynthesis/chemistry; Animals; Biogenesis; DNA, metabolism; DNA-Binding Proteins, chemistry/metabolism; Evolution; Hot Temperature; Iron, chemistry; Ligands; Metalloproteins, chemistry; Nucleotides, metabolism; Oceans and Seas; Polymers, metabolism; Protein Structure, Tertiary; Proteins, chemistry/physiology; Sulfur, chemistry},
  Owner                    = {ranjan},
  Pmid                     = {11282572},
  Timestamp                = {2009.09.11}
}

@Article{Toyota2009,
  Title                    = {Self-propelled oil droplets consuming ``fuel'' surfactant.},
  Author                   = {Taro Toyota and Naoto Maru and Martin M Hanczyc and Takashi Ikegami and Tadashi Sugawara},
  Journal                  = {J Am Chem Soc},
  Year                     = {2009},

  Month                    = {Apr},
  Number                   = {14},
  Pages                    = {5012--5013},
  Volume                   = {131},

  Abstract                 = {A micrometer-sized oil droplet of 4-octylaniline containing 5 mol \% of an amphiphilic catalyst exhibited a self-propelled motion, producing tiny oil droplets, in an aqueous dispersion of an amphiphilic precursor of 4-octylaniline. The tiny droplets on the surface of the self-propelled droplet were conveyed to the posterior surface and released to the aqueous solution. Thus the persistent movement becomes possible in this chemical system, because the processing of chemical energy to mechanical movement proceeds by consuming exogenous fuel, not consuming the oil droplet itself. The mechanism of the unidirectional motion is hypothesized in terms of an asymmetric interfacial tension around the surface of the oil droplet.},
  Institution              = {Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.},
  Owner                    = {ranjan},
  Pmid                     = {19351200},
  Timestamp                = {2011.05.13}
}

@Article{Tran2011,
  Title                    = {Solid-phase submonomer synthesis of peptoid polymers and their self-assembly into highly-ordered nanosheets.},
  Author                   = {Tran, Helen and Gael, Sarah L. and Connolly, Michael D. and Zuckermann, Ronald N.},
  Journal                  = {J Vis Exp},
  Year                     = {2011},
  Number                   = {57},
  Pages                    = {e3373},

  Abstract                 = {Peptoids are a novel class of biomimetic, non-natural, sequence-specific heteropolymers that resist proteolysis, exhibit potent biological activity, and fold into higher order nanostructures. Structurally similar to peptides, peptoids are poly N-substituted glycines, where the side chains are attached to the nitrogen rather than the alpha-carbon. Their ease of synthesis and structural diversity allows testing of basic design principles to drive de novo design and engineering of new biologically-active and nanostructured materials. Here, a simple manual peptoid synthesis protocol is presented that allows the synthesis of long chain polypeptoids (up to 50mers) in excellent yields. Only basic equipment, simple techniques (e.g. liquid transfer, filtration), and commercially available reagents are required, making peptoids an accessible addition to many researchers' toolkits. The peptoid backbone is grown one monomer at a time via the submonomer method which consists of a two-step 
monomer addition cycle: acylation and displacement. First, bromoacetic acid activated in situ with N,N'-diisopropylcarbodiimide acylates a resin-bound secondary amine. Second, nucleophilic displacement of the bromide by a primary amine follows to introduce the side chain. The two-step cycle is iterated until the desired chain length is reached. The coupling efficiency of this two-step cycle routinely exceeds 98\% and enables the synthesis of peptoids as long as 50 residues. Highly tunable, precise and chemically diverse sequences are achievable with the submonomer method as hundreds of readily available primary amines can be directly incorporated. Peptoids are emerging as a versatile biomimetic material for nanobioscience research because of their synthetic flexibility, robustness, and ordering at the atomic level. The folding of a single-chain, amphiphilic, information-rich polypeptoid into a highly-ordered nanosheet was recently demonstrated. This peptoid is a 36-mer that consists of only three different 
commercially available monomers: hydrophobic, cationic and anionic. The hydrophobic phenylethyl side chains are buried in the nanosheet core whereas the ionic amine and carboxyl side chains align on the hydrophilic faces. The peptoid nanosheets serve as a potential platform for membrane mimetics, protein mimetics, device fabrication, and sensors. Methods for peptoid synthesis, sheet formation, and microscopy imaging are described and provide a simple method to enable future peptoid nanosheet designs.},
  Doi                      = {10.3791/3373},
  Institution              = {Molecular Foundry, Lawrence Berkeley National Laboratory.},
  Keywords                 = {Nanostructures, chemistry; Peptidomimetics, chemical synthesis/chemistry; Peptoids, chemical synthesis/chemistry; Solid-Phase Synthesis Techniques, methods},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {3373},
  Pmid                     = {22083233},
  Timestamp                = {2014.05.10}
}

@Article{Trifonov2002,
  Title                    = {Molecular evolution from abiotic scratch.},
  Author                   = {Edward Trifonov and Igor Berezovsky},
  Journal                  = {FEBS Lett},
  Year                     = {2002},

  Month                    = {Sep},
  Number                   = {1-3},
  Pages                    = {1--4},
  Volume                   = {527},

  Abstract                 = {Recent papers on the emerging new theory of protein evolution are reviewed. Reconstruction of codon chronology, analysis of loop fold structure of proteins, and quantitative correspondence between optimal DNA ring closure size and protein domain size allow to outline specific stages in early protein evolution, each with its own size range.},
  Institution              = {Genome Diversity Center, Institute of Evolution, University of Haifa, 31905, Haifa, Israel. edward.trifonov@Weizmann.ac.il},
  Keywords                 = {Amino Acid Sequence; Evolution, Molecular; Genetic Code; Molecular Sequence Data; Protein Folding; Protein Structure, Tertiary; Proteins, chemistry/genetics},
  Owner                    = {ranjan},
  Pii                      = {S0014579302031654},
  Pmid                     = {12220623},
  Timestamp                = {2010.02.09}
}

@Article{Trifonov2004,
  Title                    = {The triplet code from first principles.},
  Author                   = {Trifonov, E. N.},
  Journal                  = {J Biomol Struct Dyn},
  Year                     = {2004},

  Month                    = {Aug},
  Number                   = {1},
  Pages                    = {1--11},
  Volume                   = {22},

  Abstract                 = {Temporal order ("chronology") of appearance of amino acids and their respective codons on evolutionary scene is reconstructed. A consensus chronology of amino acids is built on the basis of 60 different criteria each offering certain temporal order. After several steps of filtering the chronology vectors are averaged resulting in the consensus order: G, A, D, V, P, S, E, (L, T), R, (I, Q, N), H, K, C, F, Y, M, W. It reveals two important features: the amino acids synthesized in imitation experiments of S. Miller appeared first, while the amino acids associated with codon capture events came last. The reconstruction of codon chronology is based on the above consensus temporal order of amino acids, supplemented by the stability and complementarity rules first suggested by M. Eigen and P. Schuster, and on the earlier established processivity rule. At no point in the reconstruction the consensus amino-acid chronology was in conflict with these three rules. The derived genealogy of 
all 64 codons suggested several important predictions that are confirmed. The reconstruction of the origin and evolutionary history of the triplet code becomes, thus, a powerful research tool for molecular evolution studies, especially in its early stages.},
  Doi                      = {10.1080/07391102.2004.10506975},
  Institution              = {Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel. trifonov@research.haifa.ac.il},
  Keywords                 = {Amino Acid Sequence; Biogenesis; Chronology as Topic; Codon, history; Evolution, Molecular; History, 20th Century; Molecular Sequence Data},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {do=detail},
  Pmid                     = {15214800},
  Timestamp                = {2014.02.25}
}

@Article{Trifonov2000,
  Title                    = {Consensus temporal order of amino acids and evolution of the triplet code.},
  Author                   = {Trifonov, E. N.},
  Journal                  = {Gene},
  Year                     = {2000},

  Month                    = {Dec},
  Number                   = {1},
  Pages                    = {139--151},
  Volume                   = {261},

  Abstract                 = {Forty different single-factor criteria and multi-factor hypotheses about chronological order of appearance of amino acids in the early evolution are summarized in consensus ranking. All available knowledge and thoughts about origin and evolution of the genetic code are thus combined in a single list where the amino acids are ranked chronologically. Due to consensus nature of the chronology it has several important properties not visible in individual rankings by any of the initial criteria. Nine amino acids of the Miller's imitation of primordial environment are all ranked as topmost (G, A, V, D, E, P, S, L, T). This result does not change even after several criteria related to Miller's data are excluded from calculations. The consensus order of appearance of the 20 amino acids on the evolutionary scene also reveals a unique and strikingly simple chronological organization of 64 codons, that could not be figured out from individual criteria: New codons appear in descending order 
of their thermostability, as complementary pairs, with the complements recruited sequentially from the codon repertoires of the earlier or simultaneously appearing amino acids. These three rules (Thermostability, Complementarity and Processivity) hold strictly as well as leading position of the earliest amino acids according to Miller. The consensus chronology of amino acids, G/A, V/D, P, S, E/L, T, R, N, K, Q, I, C, H, F, M, Y, W, and the derived temporal order for codons may serve, thus, as a justified working model of choice for further studies on the origin and evolution of the genetic code.},
  Institution              = {Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel. edward.trifonov@weizmann.ac.il},
  Keywords                 = {Amino Acids, genetics; Base Composition; Codon, genetics; DNA, chemistry/genetics; Evolution, Molecular; Genetic Code, genetics; Nucleic Acid Denaturation; RNA, chemistry/genetics; Thermodynamics; Time Factors},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0378-1119(00)00476-5},
  Pmid                     = {11164045},
  Timestamp                = {2014.02.25}
}

@Article{Trus1996,
  Title                    = {The herpes simplex virus procapsid: structure, conformational changes upon maturation, and roles of the triplex proteins VP19c and VP23 in assembly.},
  Author                   = {Trus, B. L. and Booy, F. P. and Newcomb, W. W. and Brown, J. C. and Homa, F. L. and Thomsen, D. R. and Steven, A. C.},
  Journal                  = JMB,
  Year                     = {1996},
  Number                   = {3},
  Pages                    = {447--462},
  Volume                   = {263},

  File                     = {Trus1996.pdf:pdfs/Trus1996.pdf:PDF}
}

@Article{Tsai2009,
  Title                    = {Protein--protein interaction networks: how can a hub protein bind so many different partners?},
  Author                   = {Tsai, Chung-Jung and Ma, Buyong and Nussinov, Ruth},
  Journal                  = {Trends in biochemical sciences},
  Year                     = {2009},
  Number                   = {12},
  Pages                    = {594--600},
  Volume                   = {34},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.12.06}
}

@Article{Twarock2006,
  Title                    = {Mathematical virology: a novel approach to the structure and assembly of viruses},
  Author                   = {Twarock, R.},
  Journal                  = PTRSA,
  Year                     = {2006},
  Pages                    = {3357--3373},
  Volume                   = {364},

  File                     = {Twarock2006.pdf:pdfs/Twarock2006.pdf:PDF}
}

@Article{Twarock2004,
  Title                    = {A tiling approach to virus capsid assembly explaining a structural puzzle in virology},
  Author                   = {Twarock, R.},
  Journal                  = {J. Theor. Biol.},
  Year                     = {2004},
  Number                   = {4},
  Pages                    = {477--482},
  Volume                   = {226},

  File                     = {Twarock2004.pdf:pdfs/Twarock2004.pdf:PDF}
}

@Article{Uversky2011,
  Title                    = {Intrinsically disordered proteins from A to Z},
  Author                   = {Uversky, Vladimir N},
  Journal                  = {The international journal of biochemistry \& cell biology},
  Year                     = {2011},
  Number                   = {8},
  Pages                    = {1090--1103},
  Volume                   = {43},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.17}
}

@Article{Uversky2003,
  Title                    = {Protein folding revisited. A polypeptide chain at the folding-misfolding-nonfolding cross-roads: which way to go?},
  Author                   = {Uversky, V. N.},
  Journal                  = {Cell Mol Life Sci},
  Year                     = {2003},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {1852--1871},
  Volume                   = {60},

  Abstract                 = {The structure-function paradigm claims that a specific function of a protein is determined by its unique and rigid three-dimensional (3D) structure. Thus, following its biosynthesis on the ribosome, a protein must fold to be functional. This idea represents one of the cornerstones of modern biology. Numerous cases when, due to the effect of environmental factors or because of genetic defects (mutations), a polypeptide chain has lost its capability to gain a proper functional 3D structure (i.e. became misfolded), seem to confirm this concept. Consequences of such misfolding are well known and represent lost of function, aggregation, development of conformational disorders and cell death. However, the recent revelation of countless examples of intrinsically disordered proteins has cast doubt on the general validity of the structure-function paradigm and revealed an intriguing route of functional disorder. Thus, in a living cell, a polypeptide chain chooses between three potential 
fates - functional folding, potentially deadly misfolding and mysterious nonfolding. This choice is dictated by the peculiarities of amino acid sequence and/or by the pressure of environmental factors. The aim of the present review is to outline some interesting features of these three routes.},
  Institution              = {Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia. uversky@hydrogen.ucsc.edu},
  Keywords                 = {Amino Acid Sequence; Amyloid, chemistry/metabolism; Animals; Humans; Nerve Tissue Proteins, chemistry/metabolism; Protein Conformation; Protein Denaturation; Protein Folding; Synucleins; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {14523548},
  Timestamp                = {2012.09.26}
}

@Article{Uversky2002,
  Title                    = {Natively unfolded proteins: a point where biology waits for physics.},
  Author                   = {Vladimir N Uversky},
  Journal                  = {Protein Sci},
  Year                     = {2002},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {739--756},
  Volume                   = {11},

  Abstract                 = {The experimental material accumulated in the literature on the conformational behavior of intrinsically unstructured (natively unfolded) proteins was analyzed. Results of this analysis showed that these proteins do not possess uniform structural properties, as expected for members of a single thermodynamic entity. Rather, these proteins may be divided into two structurally different groups: intrinsic coils, and premolten globules. Proteins from the first group have hydrodynamic dimensions typical of random coils in poor solvent and do not possess any (or almost any) ordered secondary structure. Proteins from the second group are essentially more compact, exhibiting some amount of residual secondary structure, although they are still less dense than native or molten globule proteins. An important feature of the intrinsically unstructured proteins is that they undergo disorder-order transition during or prior to their biological function. In this respect, the Protein Quartet model,
 with function arising from four specific conformations (ordered forms, molten globules, premolten globules, and random coils) and transitions between any two of the states, is discussed.},
  File                     = {Uversky2002.pdf:pdfs/Uversky2002.pdf:PDF},
  Institution              = {Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia. uversky@hydrogen.ucsc.edu},
  Keywords                 = {Databases, Factual; Models, Chemical; Physical Phenomena; Physics; Protein Conformation; Protein Folding; Proteins, chemistry},
  Owner                    = {ranjan},
  Pmid                     = {11910019},
  Timestamp                = {2009.11.27}
}

@Article{Uversky2010,
  Title                    = {Understanding protein non-folding.},
  Author                   = {Vladimir N Uversky and A. Keith Dunker},
  Journal                  = {Biochim Biophys Acta},
  Year                     = {2010},

  Month                    = {Jun},
  Number                   = {6},
  Pages                    = {1231--1264},
  Volume                   = {1804},

  Abstract                 = {This review describes the family of intrinsically disordered proteins, members of which fail to form rigid 3-D structures under physiological conditions, either along their entire lengths or only in localized regions. Instead, these intriguing proteins/regions exist as dynamic ensembles within which atom positions and backbone Ramachandran angles exhibit extreme temporal fluctuations without specific equilibrium values. Many of these intrinsically disordered proteins are known to carry out important biological functions which, in fact, depend on the absence of a specific 3-D structure. The existence of such proteins does not fit the prevailing structure-function paradigm, which states that a unique 3-D structure is a prerequisite to function. Thus, the protein structure-function paradigm has to be expanded to include intrinsically disordered proteins and alternative relationships among protein sequence, structure, and function. This shift in the paradigm represents a major 
breakthrough for biochemistry, biophysics and molecular biology, as it opens new levels of understanding with regard to the complex life of proteins. This review will try to answer the following questions: how were intrinsically disordered proteins discovered? Why don't these proteins fold? What is so special about intrinsic disorder? What are the functional advantages of disordered proteins/regions? What is the functional repertoire of these proteins? What are the relationships between intrinsically disordered proteins and human diseases?},
  Institution              = {Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. vuversky@iupui.edu},
  Owner                    = {ranjan},
  Pii                      = {S1570-9639(10)00032-4},
  Pmid                     = {20117254},
  Timestamp                = {2010.05.01}
}

@Article{Uversky2009,
  Title                    = {Biophysics of Parkinsons Disease: Structure and Aggregation of-Synuclein},
  Author                   = {Uversky, Vladimir N and Eliezer, David},
  Journal                  = {Current Protein and Peptide Science},
  Year                     = {2009},
  Number                   = {5},
  Pages                    = {483--499},
  Volume                   = {10},

  Owner                    = {ranjan},
  Publisher                = {Bentham Science Publishers},
  Timestamp                = {2013.11.17}
}

@Article{Uversky2000a,
  Title                    = {Why are ``natively unfolded'' proteins unstructured under physiologic conditions?},
  Author                   = {V. N. Uversky and J. R. Gillespie and A. L. Fink},
  Journal                  = {Proteins},
  Year                     = {2000},

  Month                    = {Nov},
  Number                   = {3},
  Pages                    = {415--427},
  Volume                   = {41},

  Abstract                 = {"Natively unfolded" proteins occupy a unique niche within the protein kingdom in that they lack ordered structure under conditions of neutral pH in vitro. Analysis of amino acid sequences, based on the normalized net charge and mean hydrophobicity, has been applied to two sets of proteins: small globular folded proteins and "natively unfolded" ones. The results show that "natively unfolded" proteins are specifically localized within a unique region of charge-hydrophobicity phase space and indicate that a combination of low overall hydrophobicity and large net charge represent a unique structural feature of "natively unfolded" proteins.},
  Institution              = {Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. uversky@hydrogen.ucsc.edu},
  Keywords                 = {Databases, Factual; Models, Chemical; Nerve Tissue Proteins, chemistry; Protein Conformation; Protein Folding; Synucleins},
  Owner                    = {ranjan},
  Pii                      = {3.0.CO;2-7},
  Pmid                     = {11025552},
  Timestamp                = {2011.03.03}
}

@Article{Uversky2000,
  Title                    = {Zn(2+)-mediated structure formation and compaction of the ``natively unfolded'' human prothymosin alpha.},
  Author                   = {V. N. Uversky and J. R. Gillespie and I. S. Millett and A. V. Khodyakova and R. N. Vasilenko and A. M. Vasiliev and I. L. Rodionov and G. D. Kozlovskaya and D. A. Dolgikh and A. L. Fink and S. Doniach and E. A. Permyakov and V. M. Abramov},
  Journal                  = {Biochem Biophys Res Commun},
  Year                     = {2000},

  Month                    = {Jan},
  Number                   = {2},
  Pages                    = {663--668},
  Volume                   = {267},

  Abstract                 = {Human recombinant prothymosin alpha (ProTalpha) is known to have coil-like conformation at neutral pH; i.e., it belongs to the class of "natively unfolded" proteins. By means of circular dichroism, SAXS, and ANS fluorescence, we have investigated the effect of several divalent cations on the structure of this protein. Results of these studies are consistent with the conclusion that ProTalpha conformation is unaffected by large excess of Ca(2+), Mg(2+), Mn(2+), Cu(2+), and Ni(2+). However, Zn(2+) induces compaction and considerable rearrangement of the protein structure. This means that ProTalpha can specifically interact with Zn(2+) (K(D) approximately 10(-3) M), and such interactions induce folding of the natively unfolded protein into a compact partially folded (premolten globule-like) conformation. It is possible that these structural changes may be important for the function of this protein.},
  Institution              = {Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, 142292, Russia. uversky@hydrogen.ucsc.edu},
  Keywords                 = {Amino Acid Sequence; Binding Sites; Cations, Divalent, pharmacology; Circular Dichroism; Humans; Kinetics; Molecular Sequence Data; Peptide Fragments, chemistry/genetics; Protein Conformation, drug effects; Protein Folding; Protein Precursors, chemistry/genetics/metabolism; Protein Structure, Secondary; Recombinant Proteins, chemistry/genetics/metabolism; Scattering, Radiation; Sequence Homology, Amino Acid; Spectrometry, Fluorescence; Thymosin, analogs /&/ derivatives/chemistry/genetics/metabolism; Zinc, metabolism/pharmacology},
  Owner                    = {ranjan},
  Pii                      = {S0006-291X(99)92013-2},
  Pmid                     = {10631119},
  Timestamp                = {2010.04.15}
}

@Article{Uversky2008,
  Title                    = {Intrinsically disordered proteins in human diseases: introducing the D2 concept.},
  Author                   = {Uversky, Vladimir N. and Oldfield, Christopher J. and Dunker, A Keith},
  Journal                  = {Annu Rev Biophys},
  Year                     = {2008},
  Pages                    = {215--246},
  Volume                   = {37},

  Abstract                 = {Intrinsically disordered proteins (IDPs) lack stable tertiary and/or secondary structures under physiological conditions in vitro. They are highly abundant in nature and their functional repertoire complements the functions of ordered proteins. IDPs are involved in regulation, signaling, and control, where binding to multiple partners and high-specificity/low-affinity interactions play a crucial role. Functions of IDPs are tuned via alternative splicing and posttranslational modifications. Intrinsic disorder is a unique structural feature that enables IDPs to participate in both one-to-many and many-to-one signaling. Numerous IDPs are associated with human diseases, including cancer, cardiovascular disease, amyloidoses, neurodegenerative diseases, and diabetes. Overall, intriguing interconnections among intrinsic disorder, cell signaling, and human diseases suggest that protein conformational diseases may result not only from protein misfolding, but also from misidentification, 
missignaling, and unnatural or nonnative folding. IDPs, such as alpha-synuclein, tau protein, p53, and BRCA1, are attractive targets for drugs modulating protein-protein interactions. From these and other examples, novel strategies for drug discovery based on IDPs have been developed. To summarize work in this area, we are introducing the D2 (disorder in disorders) concept.},
  Doi                      = {10.1146/annurev.biophys.37.032807.125924},
  Institution              = {Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA. vuversky@iupui.edu},
  Keywords                 = {Computer Simulation; Disease; Models, Chemical; Models, Molecular; Protein Denaturation; Protein Folding; Proteins, chemistry/metabolism},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {18573080},
  Timestamp                = {2013.12.12}
}

@Article{Uversky2007,
  Title                    = {Prediction of intrinsic disorder and its use in functional proteomics.},
  Author                   = {Uversky, Vladimir N. and Radivojac, Predrag and Iakoucheva, Lilia M. and Obradovic, Zoran and Dunker, A Keith},
  Journal                  = {Methods Mol Biol},
  Year                     = {2007},
  Pages                    = {69--92},
  Volume                   = {408},

  Abstract                 = {The number of experimentally verified, intrinsically disordered (ID) proteins is rapidly rising. Research is often focused on a structural characterization of a given protein, looking for several key features. However, ID proteins with their dynamic structures that interconvert on a number of time-scales are difficult targets for the majority of traditional biophysical and biochemical techniques. Structural and functional analyses of these proteins can be significantly aided by disorder predictions. The current advances in the prediction of ID proteins and the use of protein disorder prediction in the fields of molecular biology and bioinformatics are briefly overviewed herein. A method is provided to utilize intrinsic disorder knowledge to gain structural and functional information related to individual proteins, protein groups, families, classes, and even entire proteomes.},
  Institution              = {olis, USA.},
  Keywords                 = {Amino Acids, analysis; Binding Sites; Computational Biology; Databases, Protein; Humans; Phosphorylation; Protein Folding; Proteins, chemistry/metabolism; Proteomics, statistics /&/ numerical data; Software},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {18314578},
  Timestamp                = {2013.12.08}
}

@Article{Vertessy2011,
  Title                    = {From ``fluctuation fit'' to ``conformational selection'': evolution, rediscovery, and integration of a concept},
  Author                   = {V{\'e}rtessy, Be{\'a}ta G and Orosz, Ferenc},
  Journal                  = {Bioessays},
  Year                     = {2011},
  Number                   = {1},
  Pages                    = {30--34},
  Volume                   = {33},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2013.11.17}
}

@Article{Valeriani2005,
  Title                    = {Rate of homogeneous crystal nucleation in molten NaCl},
  Author                   = {Valeriani, C and Sanz, E and Frenkel, D},
  Journal                  = {The Journal of chemical physics},
  Year                     = {2005},
  Number                   = {19},
  Pages                    = {194501},
  Volume                   = {122},

  Owner                    = {ranjan},
  Publisher                = {AIP Publishing},
  Timestamp                = {2015.04.20}
}

@Article{Valeriani2005a,
  Title                    = {Rate of homogeneous crystal nucleation in molten NaCl},
  Author                   = {Valeriani, C and Sanz, E and Frenkel, D},
  Journal                  = {The Journal of chemical physics},
  Year                     = {2005},
  Number                   = {19},
  Pages                    = {194501},
  Volume                   = {122},

  Owner                    = {ranjan},
  Publisher                = {AIP Publishing},
  Timestamp                = {2015.04.20}
}

@Article{VanWorkum2006,
  Title                    = {Symmetry, equivalence, and molecular self-assembly},
  Author                   = {Van Workum, K. and Douglas, J. F.},
  Journal                  = PRE,
  Year                     = {2006},
  Pages                    = {031502},
  Volume                   = {73},

  File                     = {VanWorkum2006.pdf:pdfs/VanWorkum2006.pdf:PDF}
}

@Article{Vandenbosch1996,
  Title                    = {Large odd–even effect in RbC n cluster size distributions},
  Author                   = {R. Vandenbosch and D. I. Will},
  Journal                  = {J. Chem. Phys.},
  Year                     = {1996},
  Pages                    = {5600-5603},
  Volume                   = {104},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Vanommeslaeghe2010,
  Title                    = {CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.},
  Author                   = {Vanommeslaeghe, K. and Hatcher, E. and Acharya, C. and Kundu, S. and Zhong, S. and Shim, J. and Darian, E. and Guvench, O. and Lopes, P. and Vorobyov, I. and Mackerell, Jr, AD},
  Journal                  = {J Comput Chem},
  Year                     = {2010},

  Month                    = {Mar},
  Number                   = {4},
  Pages                    = {671--690},
  Volume                   = {31},

  Abstract                 = {The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field 
as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.},
  Institution              = {Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA.},
  Keywords                 = {Computer Simulation; Models, Chemical; Models, Molecular; Molecular Dynamics Simulation; Pyrrolidines, chemistry; Quantum Theory; Software},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {19575467},
  Timestamp                = {2012.06.21}
}

@Article{Vasas2012,
  Title                    = {Evolution before genes.},
  Author                   = {Vasas, Vera and Fernando, Chrisantha and Santos, Mauro and Kauffman, Stuart and Szathm{\'a}ry, E{\"o}rs},
  Journal                  = {Biol Direct},
  Year                     = {2012},
  Pages                    = {1},
  Volume                   = {7},

  Abstract                 = {Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. However, this is exactly the kind of scheme we propose for how Darwinian evolution could have occurred prior to template replication.We cannot confirm previous claims that autocatalytic sets of organic polymer molecules could undergo evolution in any interesting sense by themselves. While we and others have previously imagined inhibition would result in selectability, we found that it produced multiple attractors in an autocatalytic set that cannot be selected for. Instead, we discovered that if general conditions are satisfied, the accumulation of adaptations in chemical reaction networks can occur. These conditions are the existence of rare reactions producing viable cores (
analogous to a genotype), that sustains a molecular periphery (analogous to a phenotype).We conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur.This article was reviewed by William Martin and Eugene Koonin.},
  Institution              = {Departament de Gen{\`e}tica i de Microbiologia, Grup de Biologia Evolutiva (GBE), Universitat Aut{\`o}noma de Barcelona, 08193 Bellaterra, Barcelona, Spain.},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {1745-6150-7-1},
  Pmid                     = {22221860},
  Timestamp                = {2012.04.07}
}

@Article{Venditti2006,
  Title                    = {Detecting the node-density artifact in phylogeny reconstruction.},
  Author                   = {Chris Venditti and Andrew Meade and Mark Pagel},
  Journal                  = {Syst Biol},
  Year                     = {2006},

  Month                    = {Aug},
  Number                   = {4},
  Pages                    = {637--643},
  Volume                   = {55},

  Abstract                 = {The node-density effect is an artifact of phylogeny reconstruction that can cause branch lengths to be underestimated in areas of the tree with fewer taxa. Webster, Payne, and Pagel (2003, Science 301:478) introduced a statistical procedure (the "delta" test) to detect this artifact, and here we report the results of computer simulations that examine the test's performance. In a sample of 50,000 random data sets, we find that the delta test detects the artifact in 94.4\% of cases in which it is present. When the artifact is not present (n = 10,000 simulated data sets) the test showed a type I error rate of approximately 1.69\%, incorrectly reporting the artifact in 169 data sets. Three measures of tree shape or "balance" failed to predict the size of the node-density effect. This may reflect the relative homogeneity of our randomly generated topologies, but emphasizes that nearly any topology can suffer from the artifact, the effect not being confined only to highly unevenly 
sampled or otherwise imbalanced trees. The ability to screen phylogenies for the node-density artifact is important for phylogenetic inference and for researchers using phylogenetic trees to infer evolutionary processes, including their use in molecular clock dating.},
  Institution              = {School of Biological Sciences, University of Reading, Whiteknights RG6 6AJ, Reading, England.},
  Keywords                 = {Classification, methods; Computer Simulation; Data Interpretation, Statistical; Evolution, Molecular; Models, Genetic; Phylogeny; Research Design},
  Owner                    = {ranjan},
  Pmid                     = {16969939},
  Timestamp                = {2011.04.26}
}

@Article{Venditti2010,
  Title                    = {Speciation as an active force in promoting genetic evolution.},
  Author                   = {Chris Venditti and Mark Pagel},
  Journal                  = {Trends Ecol Evol},
  Year                     = {2010},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {14--20},
  Volume                   = {25},

  Abstract                 = {There is a growing appreciation among evolutionary biologists that the rate and tempo of molecular evolution might often be altered at or near the time of speciation, i.e. that speciation is in some way a special time for genes. Molecular phylogenies frequently reveal increased rates of genetic evolution associated with speciation and other lines of investigation suggest that various types of abrupt genomic disruption can play an important role in promoting speciation via reproductive isolation. These phenomena are in conflict with the gradual view of molecular evolution that is implicit in much of our thinking about speciation and in the tools of modern biology. This raises the prospect of studying the molecular evolutionary consequences of speciation per se and studying the footprint of speciation as an active force in promoting genetic divergence. Here we discuss the reasons to believe that speciation can play such a role and elaborate on possible mechanisms for accelerated 
rates of evolution following speciation. We provide an example of how it is possible detect whether accelerated bursts of evolution occur in neutral and/or adaptive regions of genes and discuss the implications of rapid episodes of change for conventional models of molecular evolution. Speciation might often owe more to ephemeral and essentially arbitrary events that cause reproductive isolation than to the gradual and regular tug of natural selection that draws a species into a new niche.},
  Institution              = {School of Biological Sciences, University of Reading, Reading RG6 6BX, UK.},
  Keywords                 = {Animals; Evolution, Molecular; Genetic Speciation; Phylogeny},
  Owner                    = {ranjan},
  Pii                      = {S0169-5347(09)00222-5},
  Pmid                     = {19720426},
  Timestamp                = {2011.04.26}
}

@Article{Venditti2008,
  Title                    = {Model misspecification not the node-density artifact},
  Author                   = {Chris Venditti and Mark Pagel},
  Journal                  = {Evolution},
  Year                     = {2008},
  Number                   = {8},
  Pages                    = {2125--2126},
  Volume                   = {62},

  File                     = {:/home/ranjan/research/jabref/pdfs/Venditti2008.pdf:PDF},
  Owner                    = {ranjan},
  Timestamp                = {2011.04.27}
}

@Article{Verkhivker2003,
  Title                    = {Simulating disorder--order transitions in molecular recognition of unstructured proteins: where folding meets binding},
  Author                   = {Verkhivker, Gennady M and Bouzida, Djamal and Gehlhaar, Daniel K and Rejto, Paul A and Freer, Stephan T and Rose, Peter W},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2003},
  Number                   = {9},
  Pages                    = {5148--5153},
  Volume                   = {100},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2013.11.21}
}

@Article{Vishnoi2010,
  Title                    = {Young proteins experience more variable selection pressures than old proteins.},
  Author                   = {Anchal Vishnoi and Sergey Kryazhimskiy and Georgii A Bazykin and Sridhar Hannenhalli and Joshua B Plotkin},
  Journal                  = {Genome Res},
  Year                     = {2010},

  Month                    = {November},
  Number                   = {11},
  Pages                    = {1574--1581},
  Volume                   = {20},

  Abstract                 = {It is well known that young proteins tend to experience weaker purifying selection and evolve more quickly than old proteins. Here, we show that, in addition, young proteins tend to experience more variable selection pressures over time than old proteins. We demonstrate this pattern in three independent taxonomic groups: yeast, Drosophila, and mammals. The increased variability of selection pressures on young proteins is highly significant even after controlling for the fact that young proteins are typically shorter and experience weaker purifying selection than old proteins. The majority of our results are consistent with the hypothesis that the function of a young gene tends to change over time more readily than that of an old gene. At the same time, our results may be caused in part by young genes that serve constant functions over time, but nevertheless appear to evolve under changing selection pressures due to depletion of adaptive mutations. In either case, our results 
imply that the evolution of a protein-coding sequence is partly determined by its age and origin, and not only by the phenotypic properties of the encoded protein. We discuss, via specific examples, the consequences of these findings for understanding of the sources of evolutionary novelty.},
  Institution              = {Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;},
  Owner                    = {ranjan},
  Pii                      = {gr.109595.110},
  Pmid                     = {20921233},
  Timestamp                = {2010.10.28}
}

@Article{Vliegenthart2006,
  Title                    = {Mechanical deformation of spherical viruses with icosahedral symmetry},
  Author                   = {Vliegenthart,G.A. and Gompper,G.},
  Journal                  = BPJ,
  Year                     = {2006},
  Number                   = {3},
  Pages                    = {834--841},
  Volume                   = {91},

  File                     = {Vliegenthart2006.pdf:pdfs/Vliegenthart2006.pdf:PDF}
}

@Article{Vucetic2003,
  Title                    = {Flavors of protein disorder.},
  Author                   = {Slobodan Vucetic and Celeste J Brown and A. Keith Dunker and Zoran Obradovic},
  Journal                  = {Proteins},
  Year                     = {2003},

  Month                    = {Sep},
  Number                   = {4},
  Pages                    = {573--584},
  Volume                   = {52},

  Abstract                 = {Intrinsically disordered proteins are characterized by long regions lacking 3-D structure in their native states, yet they have been so far associated with 28 distinguishable functions. Previous studies showed that protein predictors trained on disorder from one type of protein often achieve poor accuracy on disorder of proteins of a different type, thus indicating significant differences in sequence properties among disordered proteins. Important biological problems are identifying different types, or flavors, of disorder and examining their relationships with protein function. Innovative use of computational methods is needed in addressing these problems due to relative scarcity of experimental data and background knowledge related to protein disorder. We developed an algorithm that partitions protein disorder into flavors based on competition among increasing numbers of predictors, with prediction accuracy determining both the number of distinct predictors and the 
partitioning of the individual proteins. Using 145 variously characterized proteins with long (>30 amino acids) disordered regions, 3 flavors, called V, C, and S, were identified by this approach, with the V subset containing 52 segments and 7743 residues, C containing 39 segments and 3402 residues, and S containing 54 segments and 5752 residues. The V, C, and S flavors were distinguishable by amino acid compositions, sequence locations, and biological function. For the sequences in SwissProt and 28 genomes, their protein functions exhibit correlations with the commonness and usage of different disorder flavors, suggesting different flavor-function sets across these protein groups. Overall, the results herein support the flavor-function approach as a useful complement to structural genomics as a means for automatically assigning possible functions to sequences.},
  Institution              = {Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA.},
  Keywords                 = {Algorithms; Archaeal Proteins, chemistry; Bacterial Proteins, chemistry; Computational Biology, methods; Databases, Protein; Drosophila Proteins, chemistry; Fungal Proteins, chemistry; Helminth Proteins, chemistry; Plant Proteins, chemistry; Protein Conformation; Protein Folding; Protein Structure, Secondary; Proteins, chemistry; Reproducibility of Results},
  Owner                    = {ranjan},
  Pmid                     = {12910457},
  Timestamp                = {2010.05.01}
}

@Book{Li1991,
  Title                    = {Fundamentals of Molecular Evolution},
  Author                   = {Li W and Grauer D},
  Publisher                = {Sinauer Associates, Inc., Sunderland MA.},
  Year                     = {1991},
  Edition                  = {1},

  Owner                    = {ranjan},
  Timestamp                = {2012.09.26}
}

@Article{Wuthrich1978,
  Title                    = {Internal motion in globular proteins},
  Author                   = {W{\"u}thrich, Kurt and Wagner, Gerhard},
  Journal                  = {Trends in biochemical sciences},
  Year                     = {1978},
  Number                   = {4},
  Pages                    = {227--230},
  Volume                   = {3},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.08.15}
}

@Article{Waechtershaeuser2007,
  Title                    = {On the chemistry and evolution of the pioneer organism.},
  Author                   = {Gunter Wachtershauser},
  Journal                  = {Chem Biodivers},
  Year                     = {2007},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {584--602},
  Volume                   = {4},

  Abstract                 = {The theory of a chemo-autotrophic origin of life in a volcanic Iron-Sulfur World postulates the emergence of a pioneer organism within a flow of volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure, iron, cobalt, nickel, and other transition-metal centers with sulfido, carbonyl, cyano, and other ligands are catalytically active, and promote the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer organism is reproductive by an autocatalytic feedback effect, whereby some organic products serve as ligands for activating the catalytic metal centres whence they arise. This unitary structure-function relationship of the pioneer organism constitutes the 'Anlage' for two major strands of evolution: enzymatization and cellularization, whereby the upward evolution 
of life by increase of molecular complexity is grounded ultimately in the transition metal-catalyzed, synthetic redox chemistry of the pioneer organism.},
  Institution              = {gwmunich@yahoo.com},
  Keywords                 = {Biogenesis; Carbon Dioxide; Carbon Monoxide; Evolution; Evolution, Molecular; Iron; Sulfur; Time},
  Owner                    = {ranjan},
  Pmid                     = {17443873},
  Timestamp                = {2009.11.29}
}

@Article{Wang2013,
  Title                    = {Somatic hypermutation maintains antibody thermodynamic stability during affinity maturation},
  Author                   = {Wang, Feng and Sen, Shiladitya and Zhang, Yong and Ahmad, Insha and Zhu, Xueyong and Wilson, Ian A and Smider, Vaughn V and Magliery, Thomas J and Schultz, Peter G},
  Journal                  = {Proceedings of the National Academy of Sciences},
  Year                     = {2013},
  Number                   = {11},
  Pages                    = {4261--4266},
  Volume                   = {110},

  Owner                    = {ranjan},
  Publisher                = {National Acad Sciences},
  Timestamp                = {2013.12.03}
}

@Article{Wang2006,
  Title                    = {On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors.},
  Author                   = {Wang, Huai-Chun and Susko, Edward and Roger, Andrew J.},
  Journal                  = {Biochem Biophys Res Commun},
  Year                     = {2006},

  Month                    = {Apr},
  Number                   = {3},
  Pages                    = {681--684},
  Volume                   = {342},

  Abstract                 = {The correlation between genomic G+C content and optimal growth temperature in prokaryotes has gained renewed interest after Musto et al. [H. Musto, H. Naya, A. Zavala, H. Romero, F. Alvarex-Valin, G. Bernardi, Correlations between genomic GC levels and optimal growth temperatures in prokaryotes, FEBS Lett. 573 (2004) 73-77], reported that positive correlations exist in 15 families studied. We have reanalyzed their data and found that when genome size and data quality were adjusted for, there was no significant evidence of relationship between optimal temperature and GC content for two of the families that had previously shown strongly significant correlations. Using updated temperature optima for Halobacteriaceae species we found the correlation is insignificant in this family. For the family Enterobacteriaceae when genome size and optimal temperature are included in a multiple linear regression, only genome size is significant as a predictor of GC content. We showed that more 
profound statistical methods than simple two factor correlation analysis should be used for analyzing complex intrinsic and extrinsic factors that affect genomic GC content. We further found that a positive correlation between temperature and genomic GC is only evident in free-living species of low optimal growth temperatures.},
  Institution              = {Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada B3H 3J5. hcwang@mathstat.dal.ca},
  Keywords                 = {Base Composition, genetics; Enterobacteriaceae, genetics/growth /&/ development; Genome, Bacterial, genetics; Prokaryotic Cells, metabolism; Temperature},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0006-291X(06)00321-4},
  Pmid                     = {16499870},
  Timestamp                = {2012.09.26}
}

@Article{Wang2003,
  Title                    = {Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding},
  Author                   = {Wang, Jin and Verkhivker, Gennady M},
  Journal                  = {Physical review letters},
  Year                     = {2003},
  Number                   = {18},
  Pages                    = {188101},
  Volume                   = {90},

  Owner                    = {ranjan},
  Publisher                = {APS},
  Timestamp                = {2014.09.02}
}

@Article{Wang2011,
  Title                    = {Reductive evolution of proteomes and protein structures.},
  Author                   = {Wang, Minglei and Kurland, Charles G. and Caetano-Anoll{\'{e}}s, Gustavo},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2011},

  Month                    = {Jul},
  Number                   = {29},
  Pages                    = {11954--11958},
  Volume                   = {108},

  Abstract                 = {The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P < 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically disordered regions as well. Reductively evolved linker sequence lengths in growth rate maximized cells should be proportional to proteome diversity. By using total in-frame coding capacity of a genome [i.e., coding sequence (CDS)] as a reliable 
measure of proteome diversity, we find linker lengths of prokaryotes clearly evolve in proportion to CDS values, whereas those of eukaryotes are more randomly larger than expected. Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not.},
  Doi                      = {10.1073/pnas.1017361108},
  Institution              = {Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.},
  Keywords                 = {Amino Acid Sequence, genetics; Computational Biology; Evolution, Molecular; Genetic Variation; Protein Structure, Tertiary; Proteome, genetics; Proteomics, methods; Species Specificity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {1017361108},
  Pmid                     = {21730144},
  Timestamp                = {2014.02.24}
}

@Article{Wang2013a,
  Title                    = {Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein.},
  Author                   = {Wang, Yong and Chu, Xiakun and Longhi, Sonia and Roche, Philippe and Han, Wei and Wang, Erkang and Wang, Jin},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2013},

  Month                    = {Oct},
  Number                   = {40},
  Pages                    = {E3743--E3752},
  Volume                   = {110},

  Abstract                 = {Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. Here, we quantified the unbound ensembles of the α-MoRE within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein. We developed a multiscaled approach by combining a physics-based and an atomic hybrid model to decipher the mechanism by which the α-MoRE interacts with the X domain of the measles virus phosphoprotein. Our multiscaled approach led to remarkable qualitative and quantitative agreements between the theoretical predictions and experimental results (e.g., chemical shifts). We found that the free α-MoRE rapidly interconverts between multiple discrete partially helical conformations and the unfolded state, in accordance with the 
experimental observations. We quantified the underlying global folding-binding landscape. This leads to a synergistic mechanism in which the recognition event proceeds via (minor) conformational selection, followed by (major) induced folding. We also provided evidence that the α-MoRE is a compact molten globule-like IDP and behaves as a downhill folder in the induced folding process. We further provided a theoretical explanation for the inherent connections between "downhill folding," "molten globule," and "intrinsic disorder" in IDP-related systems. Particularly, we proposed that binding and unbinding of IDPs proceed in a stepwise way through a "kinetic divide-and-conquer" strategy that confers them high specificity without high affinity.},
  Doi                      = {10.1073/pnas.1308381110},
  Institution              = {State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {1308381110},
  Pmid                     = {24043820},
  Timestamp                = {2013.12.14}
}

@Article{Ward2004,
  Title                    = {Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.},
  Author                   = {Ward, J. J. and Sodhi, J. S. and McGuffin, L. J. and Buxton, B. F. and Jones, D. T.},
  Journal                  = {J Mol Biol},
  Year                     = {2004},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {635--645},
  Volume                   = {337},

  Abstract                 = {An automatic method for recognizing natively disordered regions from amino acid sequence is described and benchmarked against predictors that were assessed at the latest critical assessment of techniques for protein structure prediction (CASP) experiment. The method attains a Wilcoxon score of 90.0, which represents a statistically significant improvement on the methods evaluated on the same targets at CASP. The classifier, DISOPRED2, was used to estimate the frequency of native disorder in several representative genomes from the three kingdoms of life. Putative, long (>30 residue) disordered segments are found to occur in 2.0\% of archaean, 4.2\% of eubacterial and 33.0\% of eukaryotic proteins. The function of proteins with long predicted regions of disorder was investigated using the gene ontology annotations supplied with the Saccharomyces genome database. The analysis of the yeast proteome suggests that proteins containing disorder are often located in the cell nucleus and 
are involved in the regulation of transcription and cell signalling. The results also indicate that native disorder is associated with the molecular functions of kinase activity and nucleic acid binding.},
  Institution              = {Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK.},
  Keywords                 = {Databases, Genetic; Genome; Genome, Bacterial; Genome, Fungal; Models, Molecular; Protein Conformation; Proteins, chemistry},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0022283604001482},
  Pmid                     = {15019783},
  Timestamp                = {2012.09.10}
}

@Article{Weber1975,
  Title                    = {Energetics of ligand binding to proteins.},
  Author                   = {G. Weber},
  Journal                  = {Adv Protein Chem},
  Year                     = {1975},
  Pages                    = {1--83},
  Volume                   = {29},

  Keywords                 = {Anilino Naphthalenesulfonates; Animals; Binding Sites; Calorimetry; Cattle; Kinetics; Ligands; Macromolecular Substances; Mathematics; Protein Binding; Protein Conformation; Serum Albumin, Bovine; Temperature; Thermodynamics},
  Owner                    = {ranjan},
  Pmid                     = {1136898},
  Timestamp                = {2010.05.01}
}

@Article{Webster2004,
  Title                    = {Response to Comments on ``Molecular Phylogenies Link Rates of Evolution and Speciation''.},
  Author                   = {Andrea J Webster and Robert J H Payne and Mark Pagel},
  Journal                  = {Science},
  Year                     = {2004},

  Month                    = {Jan},
  Number                   = {5655},
  Pages                    = {173c},
  Volume                   = {303},

  File                     = {:/home/ranjan/research/jabref/pdfs/Webster2004.pdf:PDF},
  Owner                    = {ranjan}
}

@Article{Webster2003,
  Title                    = {Molecular phylogenies link rates of evolution and speciation.},
  Author                   = {Andrea J Webster and Robert J H Payne and Mark Pagel},
  Journal                  = {Science},
  Year                     = {2003},

  Month                    = {Jul},
  Number                   = {5632},
  Pages                    = {478},
  Volume                   = {301},

  File                     = {:/home/ranjan/research/jabref/pdfs/Webster2003.pdf:PDF},
  Institution              = {School of Animal and Microbial Sciences, University of Reading, UK.},
  Keywords                 = {Animals; Biological Evolution; Evolution, Molecular; Genes; Likelihood Functions; Mathematics; Models, Statistical; Phylogeny},
  Owner                    = {ranjan},
  Pii                      = {301/5632/478},
  Pmid                     = {12881561},
  Timestamp                = {2011.04.26}
}

@Article{Wei2003,
  Title                    = {Contribution to stability and folding of a buried polar residue at the CARM1 methylation site of the KIX domain of CBP.},
  Author                   = {Yu Wei and Jia-Cherng Horng and Andrew C Vendel and Daniel P Raleigh and Kevin J Lumb},
  Journal                  = {Biochemistry},
  Year                     = {2003},

  Month                    = {Jun},
  Number                   = {23},
  Pages                    = {7044--7049},
  Volume                   = {42},

  Abstract                 = {The transcriptional coactivator and acetyltransferase CREB Binding Protein (CBP) is comprised of several autonomously folded and functionally independent domains. The KIX domain mediates interactions between CBP and numerous transcriptional activators. The folded region of KIX has all the structural features of a globular protein, including three alpha-helices, two short 3(10) helices, and a well-packed hydrophobic core. KIX contains a buried cation-pi interaction between the positively charged guanidinium group of Arg 600 and the aromatic ring of Tyr 640. Arg 600 is a site for regulatory methylation by CARM1/PRMT4, which negates the CREB-binding function of the KIX domain. The role of the Arg 600-Tyr 640 buried polar interaction in specifying and stabilizing the structure of KIX was investigated by comparing the folding of wild-type KIX with the single point mutants Y640F and R600M. The Y640F mutant disrupts a hydrogen bond involving the Tyr 640 OH and the backbone of V595 but 
still allows for the cation-pi interaction while the R600M mutant disrupts the cation-pi interaction. Both wild type KIX and Y640F exhibit properties expected of native like, globular proteins such as a single oligomerization state (monomer), cooperative thermal and urea-induced unfolding transitions, and a well-packed core. In contrast, the R600M mutant has properties reminiscent of a molten globule state, including a tendency to aggregate, noncooperative thermal unfolding transition, and a loosely packed core. Thus, the buried cation-pi interaction is critical for specifying the unique cooperatively folded structure of KIX.},
  Institution              = {Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA.},
  Keywords                 = {Amino Acid Substitution; Arginine, metabolism; Binding Sites; Circular Dichroism; Cyclic AMP Response Element-Binding Protein, chemistry/genetics/metabolism; Enzyme Stability; Escherichia coli, genetics/metabolism; Hot Temperature; Methylation; Plasmids, genetics/metabolism; Protein Denaturation; Protein Folding; Protein-Arginine N-Methyltransferases, chemistry/metabolism; Recombinant Proteins, chemistry/genetics/metabolism; Spectrometry, Fluorescence, methods; Trans-Activators, chemistry/genetics/metabolism; Tyrosine, metabolism; Ultracentrifugation, methods; Urea, chemistry},
  Owner                    = {ranjan},
  Pmid                     = {12795599},
  Timestamp                = {2010.09.22}
}

@Article{Weller1996,
  Title                    = {Allozyme Diversity and Genetic Identity in Schiedea and Alsinidendron (Caryophyllaceae: Alsinoideae) in the Hawaiian Islands.},
  Author                   = {Stephen G. Weller and Ann K. Sakai and Christina Straub},
  Journal                  = {Evolution},
  Year                     = {1996},
  Number                   = {1},
  Pages                    = {23--34},
  Volume                   = {50},

  Owner                    = {ranjan},
  Timestamp                = {2011.04.26}
}

@Article{Wheeler2013,
  Title                    = {From human genome to cancer genome: the first decade},
  Author                   = {Wheeler, David A and Wang, Linghua},
  Journal                  = {Genome research},
  Year                     = {2013},
  Number                   = {7},
  Pages                    = {1054--1062},
  Volume                   = {23},

  Owner                    = {ranjan},
  Publisher                = {Cold Spring Harbor Lab},
  Timestamp                = {2016.07.17}
}

@Article{Whitelam2014a,
  Title                    = {Self-assembly at a nonequilibrium critical point},
  Author                   = {Whitelam, Stephen and Hedges, Lester O and Schmit, Jeremy D},
  Journal                  = {Physical review letters},
  Year                     = {2014},
  Number                   = {15},
  Pages                    = {155504},
  Volume                   = {112},

  Owner                    = {ranjan},
  Publisher                = {APS},
  Timestamp                = {2015.04.20}
}

@Article{Whitelam2014,
  Title                    = {The Statistical Mechanics of Dynamic Pathways to Self-assembly},
  Author                   = {Whitelam, Stephen and Jack, Robert L},
  Journal                  = {Annu Rev Phys Chem.},
  Year                     = {2015},
  Pages                    = {143--163},
  Volume                   = {66},

  Owner                    = {ranjan},
  Timestamp                = {2014.08.14}
}

@Article{Whitelam2012,
  Title                    = {Self-assembly of multicomponent structures in and out of equilibrium},
  Author                   = {Whitelam, Stephen and Schulman, Rebecca and Hedges, Lester},
  Journal                  = {Physical review letters},
  Year                     = {2012},
  Number                   = {26},
  Pages                    = {265506},
  Volume                   = {109},

  Owner                    = {ranjan},
  Publisher                = {APS},
  Timestamp                = {2015.04.21}
}

@Article{Whitney2010,
  Title                    = {Did genetic drift drive increases in genome complexity?},
  Author                   = {Kenneth D Whitney and Theodore Garland},
  Journal                  = {PLoS Genet},
  Year                     = {2010},
  Number                   = {8},
  Volume                   = {6},

  Abstract                 = {Mechanisms underlying the dramatic patterns of genome size variation across the tree of life remain mysterious. Effective population size (N(e)) has been proposed as a major driver of genome size: selection is expected to efficiently weed out deleterious mutations increasing genome size in lineages with large (but not small) N(e). Strong support for this model was claimed from a comparative analysis of N(e)u and genome size for ~30 phylogenetically diverse species ranging from bacteria to vertebrates, but analyses at that scale have so far failed to account for phylogenetic nonindependence of species. In our reanalysis, accounting for phylogenetic history substantially altered the perceived strength of the relationship between N(e)u and genomic attributes: there were no statistically significant associations between N(e)u and gene number, intron size, intron number, the half-life of gene duplicates, transposon number, transposons as a fraction of the genome, or overall genome 
size. We conclude that current datasets do not support the hypothesis of a mechanistic connection between N(e) and these genomic attributes, and we suggest that further progress requires larger datasets, phylogenetic comparative methods, more robust estimators of genetic drift, and a multivariate approach that accounts for correlations between putative explanatory variables.},
  Institution              = {Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America. kwhitney@rice.edu},
  Keywords                 = {Animals; Bacteria, classification/genetics; Eukaryota, classification/genetics; Evolution, Molecular; Fungi, classification/genetics; Genetic Drift; Genome; Humans; Introns; Models, Genetic; Phylogeny},
  Owner                    = {ranjan},
  Pmid                     = {20865118},
  Timestamp                = {2011.02.09}
}

@Article{Widmann2000,
  Title                    = {Comparison of folding rates of homologous prokaryotic and eukaryotic proteins.},
  Author                   = {Widmann, M. and Christen, P.},
  Journal                  = {J Biol Chem},
  Year                     = {2000},

  Month                    = {Jun},
  Number                   = {25},
  Pages                    = {18619--18622},
  Volume                   = {275},

  Abstract                 = {The rate of polypeptide chain elongation is up to one order of magnitude faster in prokaryotic cells than in eukaryotes. Here we report that the rates of in vitro refolding of orthologous prokaryotic and eukaryotic proteins correlate with their differential rates of biosynthesis. The mitochondrial and cytosolic aspartate aminotransferases of chicken and aspartate aminotransferase of Escherichia coli show pairwise sequence identities of 41-48\% and nearly identical three-dimensional structures. Nevertheless, the prokaryotic enzyme refolded 6 times faster (at 25 degrees C) than the eukaryotic isoenzymes after denaturation in 6 m guanidine hydrochloride. Prokaryotic malate dehydrogenase and lactate dehydrogenase also renatured faster than their orthologous eukaryotic counterparts, suggesting that evolutionary pressure has adapted the rate of folding to the rate of elongation of polypeptide chains.},
  Doi                      = {10.1074/jbc.C000156200},
  Institution              = {Biochemisches Institut der Universität Zürich, CH-8057 Zürich, Switzerland.},
  Keywords                 = {Aspartate Aminotransferases, metabolism; Bacterial Proteins, metabolism; Escherichia coli, enzymology; Eukaryotic Cells, metabolism; Prokaryotic Cells, metabolism; Protein Folding},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {C000156200},
  Pmid                     = {10781576},
  Timestamp                = {2014.02.24}
}

@Misc{SnakeWiki,
  Title                    = {Snake (video game) --- Wikipedia{,} The Free Encyclopedia},

  Author                   = {Wikipedia},
  Note                     = {[Online; accessed 30-August-2014]},
  Year                     = {2014}
}

@Article{Wikoff2006,
  Title                    = {Time-resolved molecular dynamics of bacteriophage HK97 capsid maturation interpreted by electron cryo-microscopy and X-ray crystallography},
  Author                   = {Wikoff, W. R. and Conway, J. F. and Tang, J. and Lee, K. K. and Gan, L. and Cheng, N. and Duda, R. L. and Hendrix, R. W. and Steven, A. C. and Johnson, J. E.},
  Journal                  = {J. Struct. Biol.},
  Year                     = {2006},
  Number                   = {3},
  Pages                    = {300--306},
  Volume                   = {153},

  File                     = {Wikoff2006.pdf:pdfs/Wikoff2006.pdf:PDF}
}

@Article{Wilke2003,
  Title                    = {Evolution of mutational robustness},
  Author                   = {Wilke, Claus O and Adami, Christoph},
  Journal                  = {Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis},
  Year                     = {2003},
  Number                   = {1},
  Pages                    = {3--11},
  Volume                   = {522},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.30}
}

@Article{Williams2006,
  Title                    = {Assessing the accuracy of ancestral protein reconstruction methods.},
  Author                   = {Paul D Williams and David D Pollock and Benjamin P Blackburne and Richard A Goldstein},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2006},

  Month                    = {Jun},
  Number                   = {6},
  Pages                    = {e69},
  Volume                   = {2},

  Abstract                 = {The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of "ancestral sequences" inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and 
maximum likelihood that reconstruct a "best guess" amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.},
  Institution              = {Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.},
  Keywords                 = {Algorithms; Conserved Sequence; Evolution, Molecular; Genetic Variation, genetics; Proteins, chemistry/classification/genetics; Reproducibility of Results; Sensitivity and Specificity; Sequence Alignment, methods; Sequence Analysis, Protein, methods; Sequence Homology, Amino Acid},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {05-PLCB-RA-0336R3},
  Pmid                     = {16789817},
  Timestamp                = {2011.09.03}
}

@Article{Wilson1977,
  Title                    = {Biochemical evolution.},
  Author                   = {A. C. Wilson and S. S. Carlson and T. J. White},
  Journal                  = {Annu Rev Biochem},
  Year                     = {1977},
  Pages                    = {573--639},
  Volume                   = {46},

  Keywords                 = {Amino Acid Sequence; Animals; Anura; Base Sequence; Biological Clocks; Biological Evolution; Birds; Cell Division; Cyanobacteria, physiology; DNA, metabolism; Fossils; Genes; Genetic Variation; Mammals; Models, Biological; Phylogeny; Plants; Proteins, immunology; Serum Albumin; Species Specificity; Time Factors; Transferrin},
  Owner                    = {ranjan},
  Pmid                     = {409339},
  Timestamp                = {2011.04.26}
}

@Article{Witt2004,
  Title                    = {Comment on ``Molecular phylogenies link rates of evolution and speciation'' (I).},
  Author                   = {Christopher C. Witt and Robb T. Brumfield},
  Journal                  = {Science},
  Year                     = {2004},

  Month                    = {Jan},
  Number                   = {5655},
  Pages                    = {173b},
  Volume                   = {303},

  Owner                    = {ranjan}
}

@Article{Woese1998a,
  Title                    = {The universal ancestor.},
  Author                   = {C. Woese},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1998},

  Month                    = {Jun},
  Number                   = {12},
  Pages                    = {6854--6859},
  Volume                   = {95},

  Abstract                 = {A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when "genetic temperatures" were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell "crystallized," i.e., became refractory to lateral gene transfer, at different stages of "cooling," with the translation apparatus probably 
crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.},
  Institution              = {U IL, Urbana},
  Keywords                 = {Animals; Evolution; Gene Transfer Techniques; Genes; Humans; Models, Biological},
  Owner                    = {ranjan},
  Pmid                     = {9618502},
  Timestamp                = {2009.11.28}
}

@Article{Woese2002,
  Title                    = {On the evolution of cells.},
  Author                   = {Woese, Carl R.},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2002},

  Month                    = {Jun},
  Number                   = {13},
  Pages                    = {8742--8747},
  Volume                   = {99},

  Abstract                 = {A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex 
and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given.},
  Institution              = {Department of Microbiology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, B103 Chemical and Life Sciences Laboratory, Urbana, IL 61801-3709, USA. carl@phylo.life.uiuc.edu},
  Keywords                 = {Biological Evolution; Cells; Gene Transfer, Horizontal; Protein Biosynthesis},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {132266999},
  Pmid                     = {12077305},
  Timestamp                = {2012.09.07}
}

@Article{Woese2000,
  Title                    = {Interpreting the universal phylogenetic tree.},
  Author                   = {Woese, C. R.},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2000},

  Month                    = {Jul},
  Number                   = {15},
  Pages                    = {8392--8396},
  Volume                   = {97},

  Abstract                 = {The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.},
  Institution              = {U IL, Urbana},
  Keywords                 = {Cell Size; Evolution, Molecular; Gene Transfer, Horizontal; Genetic Variation; Phylogeny; RNA, Ribosomal, classification},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {97/15/8392},
  Pmid                     = {10900003},
  Timestamp                = {2012.09.07}
}

@Article{Wolfgang2003,
  Title                    = {Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa.},
  Author                   = {Wolfgang, Matthew C. and Kulasekara, Bridget R. and Liang, Xiaoyou and Boyd, Dana and Wu, Kai and Yang, Qing and Miyada, C Garrett and Lory, Stephen},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2003},

  Month                    = {Jul},
  Number                   = {14},
  Pages                    = {8484--8489},
  Volume                   = {100},

  Abstract                 = {Pseudomonas aeruginosa is a ubiquitous environmental bacterium capable of causing a variety of life-threatening human infections. The genetic basis for preferential infection of certain immunocompromised patients or individuals with cystic fibrosis by P. aeruginosa is not understood. To establish whether variation in the genomic repertoire of P. aeruginosa strains can be associated with a particular type of infection, we used a whole-genome DNA microarray to determine the genome content of 18 strains isolated from the most common human infections and environmental sources. A remarkable conservation of genes including those encoding nearly all known virulence factors was observed. Phylogenetic analysis of strain-specific genes revealed no correlation between genome content and infection type. Clusters of strain-specific genes in the P. aeruginosa genome, termed variable segments, appear to be preferential sites for the integration of novel genetic material. A specialized cloning 
vector was developed for capture and analysis of these genomic segments. With this capture system a site associated with the strain-specific ExoU cytotoxin-encoding gene was interrogated and an 80-kb genomic island carrying exoU was identified. These studies demonstrate that P. aeruginosa strains possess a highly conserved genome that encodes genes important for survival in numerous environments and allows it to cause a variety of human infections. The acquisition of novel genetic material, such as the exoU genomic island, through horizontal gene transfer may enhance colonization and survival in different host environments.},
  Institution              = {Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.},
  Keywords                 = {Bacterial Proteins, genetics; DNA, Bacterial, genetics; Fresh Water; Gene Expression Profiling; Gene Transfer, Horizontal; Genetic Vectors, genetics; Genome, Bacterial; Humans; Oligonucleotide Array Sequence Analysis; Phylogeny; Pseudomonas Infections, microbiology; Pseudomonas aeruginosa, genetics/pathogenicity; Recombination, Genetic; Saccharomyces cerevisiae, genetics; Transformation, Genetic; Virulence, genetics; Washington; Water Microbiology},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {0832438100},
  Pmid                     = {12815109},
  Timestamp                = {2012.09.10}
}

@Article{Wong1998,
  Title                    = {Barstar has a highly dynamic hydrophobic core: evidence from molecular dynamics simulations and nuclear magnetic resonance relaxation data.},
  Author                   = {K. B. Wong and V. Daggett},
  Journal                  = {Biochemistry},
  Year                     = {1998},

  Month                    = {Aug},
  Number                   = {32},
  Pages                    = {11182--11192},
  Volume                   = {37},

  Abstract                 = {The dynamic behavior of the ribonuclease inhibitor barstar has been investigated by molecular dynamics (MD) simulations in explicit water. Two 2.5 ns MD simulations were performed, and an ensemble of 25 000 structures was generated. This ensemble reproduces the solution structures and is consistent with the experimental structural restraints from NMR spectroscopy. Reorientation of the backbone NH bond vectors and side chain methyl groups was monitored by calculation of autocorrelation functions and the generalized S2 order parameters. Order parameters derived for motion in the approximately 100 ps time scale were compared with those obtained from NMR relaxation measurements. Consistent with experiment, the backbone NH bond vectors were relatively rigid. In contrast, the side chain methyl groups exhibited a wide dynamic range, from restricted motion comparable to that of the backbone to rapid unrestricted motion. The order parameters for the methyl groups correlate well with 
their spatial separation from the backbone and are residue-type dependent. Smaller S2axis values were observed for leucine methyl groups, in part due to side chain hopping between two predominant rotamers (g+t and tg-). Motions such as the flipping of aromatic rings and the hopping of leucine side chains were prevalent within the hydrophobic core, suggesting that the core is fluid-like with low energy barriers between native conformational substates. Thus, our studies suggest that the entropy of the native state can be significant and should not be discounted in thermodynamic considerations of protein folding. On the basis of our results, the side chain motion represents the primary source of the residual entropy of the native state and entropic considerations based solely on backbone dynamics would be incomplete.},
  Institution              = {Department of Medicinal Chemistry, University of Washington, Seattle 98195-7610, USA.},
  Keywords                 = {Bacillus, enzymology; Bacterial Proteins, chemistry; Computer Simulation; Crystallography, X-Ray; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; Protein Structure, Secondary; Ribonucleases, antagonists /&/ inhibitors; Software; Solutions; Temperature; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {bi980552i},
  Pmid                     = {9698364},
  Timestamp                = {2010.02.14}
}

@Article{Workum2006,
  Title                    = {Symmetry, equivalence, and molecular self-assembly.},
  Author                   = {Kevin Van Workum and Jack F Douglas},
  Journal                  = {Phys Rev E Stat Nonlin Soft Matter Phys},
  Year                     = {2006},

  Month                    = {Mar},
  Number                   = {3 Pt 1},
  Pages                    = {031502},
  Volume                   = {73},

  Abstract                 = {Molecular self-assembly at equilibrium is fundamental to the fields of biological self-organization, the development of novel environmentally responsive polymeric materials, and nanofabrication. Our approach to understanding the principles governing this process is inspired by existing models and measurements for the self-assembly of actin, tubulin, and the ubiquitous icosahedral shell structures of viral capsids. We introduce a family of simple potentials that give rise to the self-assembly of linear polymeric, random surface ("membrane"), tubular ("nanotube"), and hollow icosahedral structures that are similar in many respects to their biological counterparts. The potentials involve equivalent particles and an interplay between directional (dipolar, multipolar) and short-range (van der Waals) interactions. Specifically, we find that the dipolar potential, having a continuous rotational symmetry about the dipolar axis, gives rise to chain formation, while particles with 
multipolar potentials, having discrete rotational symmetries (square quadrupole or triangular ring of dipoles or "hexapole"), lead to the self-assembly of open sheet, nanotube, and hollow icosahedral geometries. These changes in the geometry of self-assembly are accompanied by significant changes in the kinetics of the organization.},
  Institution              = {National Institute of Standards and Technology, Polymers Division, Gaithersburg, Maryland 20899, USA. vanw@usna.edu},
  Owner                    = {ranjan},
  Pmid                     = {16605527},
  Timestamp                = {2010.12.12}
}

@Article{Wright1996,
  Title                    = {A Monte Carlo study of methanol clusters (CH$_3$OH)$_N$ ,$N=5–256$},
  Author                   = {D. Wright and M. S. ElShall},
  Journal                  = {J. Chem. Phys.},
  Year                     = {1996},
  Pages                    = {11199--11208},
  Volume                   = {105},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Wright1994,
  Title                    = {Monte Carlo simulation of acetonitrile clusters [{CH}$_3${CN}]$_{N}$, ${N}=2-256$: Melting transitions and even! odd character of small clusters (${N}=2-9$), heat capacities, density profiles, fractal dimension, intracluster dimerization, and dipole orientation.},
  Author                   = {D. Wright and M. Samy ElShall},
  Journal                  = {J. Chern. Phys.},
  Year                     = {1994},
  Number                   = {5},
  Pages                    = {3791--3802},
  Volume                   = {100},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.17}
}

@Article{Wright2009,
  Title                    = {Linking folding and binding},
  Author                   = {Wright, Peter E and Dyson, H Jane},
  Journal                  = {Current opinion in structural biology},
  Year                     = {2009},
  Number                   = {1},
  Pages                    = {31--38},
  Volume                   = {19},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.08.25}
}

@Article{Wright1999,
  Title                    = {Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm},
  Author                   = {Wright, Peter E and Dyson, H Jane},
  Journal                  = {Journal of Molecular Biology},
  Year                     = {1999},
  Number                   = {2},
  Pages                    = {321--331},
  Volume                   = {293},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.11.21}
}

@Article{Wright1931,
  Title                    = {Evolution in Mendelian Populations.},
  Author                   = {Wright, S.},
  Journal                  = {Genetics},
  Year                     = {1931},

  Month                    = {Mar},
  Number                   = {2},
  Pages                    = {97--159},
  Volume                   = {16},

  Institution              = {University of Chicago, Chicago, Illinois.},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {17246615},
  Timestamp                = {2012.09.30}
}

@Article{Wu2010,
  Title                    = {Quantum mechanical studies on model $\alpha$-pleated sheets},
  Author                   = {Wu, Hao and Canfield, Alana and Adhikari, Jhashanath and Huo, Shuanghong},
  Journal                  = {Journal of computational chemistry},
  Year                     = {2010},
  Number                   = {6},
  Pages                    = {1216--1223},
  Volume                   = {31},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2015.11.15}
}

@Article{Wu2012,
  Title                    = {On the molecular mechanism of GC content variation among eubacterial genomes.},
  Author                   = {Wu, Hao and Zhang, Zhang and Hu, Songnian and Yu, Jun},
  Journal                  = {Biol Direct},
  Year                     = {2012},
  Pages                    = {2},
  Volume                   = {7},

  Abstract                 = {As a key parameter of genome sequence variation, the GC content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this GC content variation and its relationship to other fundamental processes. Previously, we classified eubacteria into dnaE-based groups (the dimeric combination of DNA polymerase III alpha subunits), according to a hypothesis where GC content variation is essentially governed by genome replication and DNA repair mechanisms. Further investigation led to the discovery that two major mutator genes, polC and dnaE2, may be responsible for genomic GC content variation. Consequently, an in-depth analysis was conducted to evaluate various potential intrinsic and extrinsic factors in association with GC content variation among eubacterial genomes.Mutator genes, especially those with dominant effects on the mutation spectra, are biased towards either GC or AT richness, and they alter genomic GC content 
in the two opposite directions. Increased bacterial genome size (or gene number) appears to rely on increased genomic GC content; however, it is unclear whether the changes are directly related to certain environmental pressures. Certain environmental and bacteriological features are related to GC content variation, but their trends are more obvious when analyzed under the dnaE-based grouping scheme. Most terrestrial, plant-associated, and nitrogen-fixing bacteria are members of the dnaE1|dnaE2 group, whereas most pathogenic or symbiotic bacteria in insects, and those dwelling in aquatic environments, are largely members of the dnaE1|polV group.Our studies provide several lines of evidence indicating that DNA polymerase III $\alpha$ subunit and its isoforms participating in either replication (such as polC) or SOS mutagenesis/translesion synthesis (such as dnaE2), play dominant roles in determining GC variability. Other environmental or bacteriological factors, such as genome size, temperature, oxygen 
requirement, and habitat, either play subsidiary roles or rely indirectly on different mutator genes to fine-tune the GC content. These results provide a comprehensive insight into mechanisms of GC content variation and the robustness of eubacterial genomes in adapting their ever-changing environments over billions of years.},
  Institution              = {hou 310007, China.},
  Keywords                 = {Adaptation, Biological; Bacteria, classification/genetics; Bacterial Proteins, genetics; Base Composition; DNA Polymerase III, genetics; DNA Replication; DNA, Bacterial, genetics; DNA-Directed DNA Polymerase, genetics; Ecosystem; Genes, Bacterial; Genetic Variation; Genome Size; Genome, Bacterial; Isoenzymes, genetics; Mutagenesis; Phylogeny; Temperature},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {1745-6150-7-2},
  Pmid                     = {22230424},
  Timestamp                = {2012.09.26}
}

@Article{Wu1997,
  Title                    = {Hydrophobic sequence minimization of the alpha-lactalbumin molten globule.},
  Author                   = {L. C. Wu and P. S. Kim},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1997},

  Month                    = {Dec},
  Number                   = {26},
  Pages                    = {14314--14319},
  Volume                   = {94},

  Abstract                 = {The molten globule, a widespread protein-folding intermediate, can attain a native-like backbone topology, even in the apparent absence of rigid side-chain packing. Nonetheless, mutagenesis studies suggest that molten globules are stabilized by some degree of side-chain packing among specific hydrophobic residues. Here we investigate the importance of hydrophobic side-chain diversity in determining the overall fold of the alpha-lactalbumin molten globule. We have replaced all of the hydrophobic amino acids in the sequence of the helical domain with a representative amino acid, leucine. Remarkably, the minimized molecule forms a molten globule that retains many structural features characteristic of a native alpha-lactalbumin fold. Thus, nonspecific hydrophobic interactions may be sufficient to determine the global fold of a protein.},
  File                     = {Wu1997.pdf:pdfs/Wu1997.pdf:PDF},
  Institution              = {Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA.},
  Keywords                 = {Amino Acid Sequence; Animals; Humans; Lactalbumin, chemistry/genetics; Molecular Sequence Data; Protein Folding; Sequence Analysis},
  Owner                    = {ranjan},
  Pmid                     = {9405609},
  Timestamp                = {2009.10.03}
}

@Article{Xia2008,
  Title                    = {Impacts of protein-protein interaction domains on organism and network complexity.},
  Author                   = {Kai Xia and Zheng Fu and Lei Hou and Jing-Dong J Han},
  Journal                  = {Genome Res},
  Year                     = {2008},

  Month                    = {Sep},
  Number                   = {9},
  Pages                    = {1500--1508},
  Volume                   = {18},

  Abstract                 = {It has been a puzzle that genome or proteome sizes are not correlated with the complexity of the organisms. Although alternative splicing and noncoding and regulatory elements explain some of the differences, the complexity of the protein interaction network and regulatory network may provide additional explanations. Here, we collected 642 domains that mediate protein-protein interactions (PPIs) and examined the evolution of the PPI domains and its impact on organismal complexity and PPI network complexity. In agreement with previous more general studies of protein domains, a significant expansion of PPI domains per proteome was found in metazoa. We also found both the number and coverage of PPI domains per protein increased. However, a better correlation with complexity was seen with increasing PPI domain coverage per protein, so that proteins in complex organisms are more compact and specialized in PPI. Such a structural adaptation of the proteins is correlated with the number 
of interactions that the proteins can make in PPI networks, and seems to be a more favorable way to increase network connectivity than other structural adaptations.},
  Institution              = {Chinese Academy of Sciences, Key Laboratory of Molecular Developmental Biology, Center for Molecular Systems Biology, Institute of Genetics and Developmental Biology, Beijing 100101, China.},
  Keywords                 = {Animals; Databases, Protein; Genome; Humans; Protein Interaction Domains and Motifs; Protein Interaction Mapping; Proteins, chemistry/metabolism; Proteome, metabolism; Regression Analysis},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {gr.068130.107},
  Pmid                     = {18687879},
  Timestamp                = {2011.08.03}
}

@Article{Xu2011,
  Title                    = {Path lengths in protein-protein interaction networks and biological complexity.},
  Author                   = {Ke Xu and Ivona Bezakova and Leonid Bunimovich and Soojin V Yi},
  Journal                  = {Proteomics},
  Year                     = {2011},

  Month                    = {May},
  Number                   = {10},
  Pages                    = {1857--1867},
  Volume                   = {11},

  Abstract                 = {We investigated the biological significance of path lengths in 12 protein-protein interaction (PPI) networks. We put forward three predictions, based on the idea that biological complexity influences path lengths. First, at the network level, path lengths are generally longer in PPIs than in random networks. Second, this pattern is more pronounced in more complex organisms. Third, within a PPI network, path lengths of individual proteins are biologically significant. We found that in 11 of the 12 species, average path lengths in PPI networks are significantly longer than those in randomly rewired networks. The PPI network of the malaria parasite Plasmodium falciparum, however, does not exhibit deviation from rewired networks. Furthermore, eukaryotic PPIs exhibit significantly greater deviation from randomly rewired networks than prokaryotic PPIs. Thus our study highlights the potentially meaningful variation in path lengths of PPI networks. Moreover, node eccentricity, defined 
as the longest path from a protein to others, is significantly correlated with the levels of gene expression and dispensability in the yeast PPI network. We conclude that biological complexity influences both global and local properties of path lengths in PPI networks. Investigating variation of path lengths may provide new tools to analyze the evolution of functional modules in biological systems.},
  Institution              = {School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {21480527},
  Timestamp                = {2011.07.19}
}

@Article{Xue2010,
  Title                    = {Archaic chaos: intrinsically disordered proteins in Archaea},
  Author                   = {Xue, Bin and Williams, Robert W. and Oldfield, Christopher J. and Dunker, A Keith and Uversky, Vladimir N.},
  Journal                  = {BMC Syst Biol},
  Year                     = {2010},
  Pages                    = {S1},
  Volume                   = {4 Suppl 1},

  Abstract                 = {Many proteins or their regions known as intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack unique 3D structure in their native states under physiological conditions yet fulfill key biological functions. Earlier bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. Archaea belong to an intriguing domain of life whose members, being microbes, are characterized by a unique mosaic-like combination of bacterial and eukaryotic properties and include inhabitants of some of the most extreme environments on the planet. With the expansion of the archaea genome data (more than fifty archaea species from five different phyla are known now), and with recent improvements in the accuracy of intrinsic disorder prediction, it is time to re-examine the abundance of IDPs and IDRs in the archaea domain.The abundance of IDPs 
and IDRs in 53 archaea species is analyzed. The amino acid composition profiles of these species are generally quite different from each other. The disordered content is highly species-dependent. Thermoproteales proteomes have 14\% of disordered residues, while in Halobacteria, this value increases to 34\%. In proteomes of these two phyla, proteins containing long disordered regions account for 12\% and 46\%, whereas 4\% and 26\% their proteins are wholly disordered. These three measures of disorder content are linearly correlated with each other at the genome level. There is a weak correlation between the environmental factors (such as salinity, pH and temperature of the habitats) and the abundance of intrinsic disorder in Archaea, with various environmental factors possessing different disorder-promoting strengths. Harsh environmental conditions, especially those combining several hostile factors, clearly favor increased disorder content. Intrinsic disorder is highly abundant in functional Pfam domains of 
the archaea origin. The analysis based on the disordered content and phylogenetic tree indicated diverse evolution of intrinsic disorder among various classes and species of Archaea.Archaea proteins are rich in intrinsic disorder. Some of these IDPs and IDRs likely evolve to help archaea to accommodate to their hostile habitats. Other archaean IDPs and IDRs possess crucial biological functions similar to those of the bacterial and eukaryotic IDPs/IDRs.},
  Doi                      = {10.1186/1752-0509-4-S1-S1},
  Institution              = {Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.},
  Keywords                 = {Amino Acid Sequence; Archaea, chemistry/genetics; Archaeal Proteins, chemistry/genetics/metabolism; Ecosystem; Evolution, Molecular; Models, Molecular; Molecular Sequence Data; Phylogeny; Protein Conformation; Proteomics; Species Specificity},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {1752-0509-4-S1-S1},
  Pmid                     = {20522251},
  Timestamp                = {2013.12.08}
}

@Article{Yvcas1974,
  Title                    = {On earlier states of the biochemical system},
  Author                   = {Y{\v{c}}as, Martynas},
  Journal                  = {Journal of theoretical biology},
  Year                     = {1974},
  Number                   = {1},
  Pages                    = {145--160},
  Volume                   = {44},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2013.12.04}
}

@Article{Yadid2010,
  Title                    = {Metamorphic proteins mediate evolutionary transitions of structure.},
  Author                   = {Itamar Yadid and Noam Kirshenbaum and Michal Sharon and Orly Dym and Dan S Tawfik},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2010},
  Number                   = {16},
  Pages                    = {7287-7292},
  Volume                   = {107},

  Owner                    = {ranjan},
  Timestamp                = {2010.09.02}
}

@Article{Yamada2010,
  Title                    = {A bimodal distribution of two distinct categories of intrinsically disordered structures with separate functions in FG nucleoporins.},
  Author                   = {Yamada, Justin and Phillips, Joshua L. and Patel, Samir and Goldfien, Gabriel and Calestagne-Morelli, Alison and Huang, Hans and Reza, Ryan and Acheson, Justin and Krishnan, Viswanathan V. and Newsam, Shawn and Gopinathan, Ajay and Lau, Edmond Y. and Colvin, Michael E. and Uversky, Vladimir N. and Rexach, Michael F.},
  Journal                  = {Mol Cell Proteomics},
  Year                     = {2010},

  Month                    = {Oct},
  Number                   = {10},
  Pages                    = {2205--2224},
  Volume                   = {9},

  Abstract                 = {Nuclear pore complexes (NPCs) gate the only conduits for nucleocytoplasmic transport in eukaryotes. Their gate is formed by nucleoporins containing large intrinsically disordered domains with multiple phenylalanine-glycine repeats (FG domains). In combination, these are hypothesized to form a structurally and chemically homogeneous network of random coils at the NPC center, which sorts macromolecules by size and hydrophobicity. Instead, we found that FG domains are structurally and chemically heterogeneous. They adopt distinct categories of intrinsically disordered structures in non-random distributions. Some adopt globular, collapsed coil configurations and are characterized by a low charge content. Others are highly charged and adopt more dynamic, extended coil conformations. Interestingly, several FG nucleoporins feature both types of structures in a bimodal distribution along their polypeptide chain. This distribution functionally correlates with the attractive or repulsive 
character of their interactions with collapsed coil FG domains displaying cohesion toward one another and extended coil FG domains displaying repulsion. Topologically, these bipartite FG domains may resemble sticky molten globules connected to the tip of relaxed or extended coils. Within the NPC, the crowding of FG nucleoporins and the segregation of their disordered structures based on their topology, dimensions, and cohesive character could force the FG domains to form a tubular gate structure or transporter at the NPC center featuring two separate zones of traffic with distinct physicochemical properties.},
  Doi                      = {10.1074/mcp.M000035-MCP201},
  Institution              = {Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064, USA.},
  Keywords                 = {Amino Acid Sequence; Electrophoresis, Polyacrylamide Gel; Glycine, chemistry; Molecular Sequence Data; Nuclear Pore Complex Proteins, chemistry; Phenylalanine, chemistry; Protein Conformation; Sequence Homology, Amino Acid},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {M000035-MCP201},
  Pmid                     = {20368288},
  Timestamp                = {2013.12.15}
}

@Article{Yan2005,
  Title                    = {The marine algal virus PpV01 has an icosahedral capsid with T=219 quasisymmetry},
  Author                   = {Yan,X. and Chipman,P.R. and Castberg,T. and Bratbak,G. and Baker,T.S.},
  Journal                  = {J Virol.},
  Year                     = {2005},
  Number                   = {14},
  Pages                    = {9236--9243},
  Volume                   = {79},

  File                     = {Yan2005.pdf:pdfs/Yan2005.pdf:PDF}
}

@Article{Yan2000,
  Title                    = {Structure and assembly of large lipid-containing dsDNA viruses},
  Author                   = {Yan,X. and Olson,N.H. and Van Etten,J.L. and Bergoin,M. and Rossmann,M.G. and Baker,T.S.},
  Journal                  = {Nat Struct Biol.},
  Year                     = {2000},
  Number                   = {2},
  Pages                    = {101--103},
  Volume                   = {7},

  File                     = {Yan2000.pdf:pdfs/Yan2000.pdf:PDF}
}

@Article{Yi2005,
  Title                    = {Genome size is negatively correlated with effective population size in ray-finned fish.},
  Author                   = {Yi, Soojin and Streelman, J Todd},
  Journal                  = {Trends Genet},
  Year                     = {2005},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {643--646},
  Volume                   = {21},

  Abstract                 = {A recent theory suggesting that genome size and complexity can increase as a passive consequence of small effective population size has generated much controversy. In this article, we demonstrate that freshwater fish species, which have smaller effective population sizes than marine fish species, have larger genomes. We show that genome size is negatively correlated with genetic variability, independent of phylogeny, body size and generation time. Genome duplication is also observed predominantly in freshwater fish. These results suggest that the raw materials of complexity originate under conditions of reduced selection efficiency.},
  Institution              = {School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA. soojin.yi@biology.gatech.edu},
  Keywords                 = {Animals; Fishes, genetics; Fresh Water; Genetic Variation; Genome; Heterozygote; Oceans and Seas; Phylogeny; Population, genetics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0168-9525(05)00268-4},
  Pmid                     = {16213058},
  Timestamp                = {2012.09.30}
}

@Article{Yoo2008,
  Title                    = {Peptoid architectures: elaboration, actuation, and application},
  Author                   = {Yoo, Barney and Kirshenbaum, Kent},
  Journal                  = {Current opinion in chemical biology},
  Year                     = {2008},
  Number                   = {6},
  Pages                    = {714--721},
  Volume                   = {12},

  Owner                    = {ranjan},
  Publisher                = {Elsevier},
  Timestamp                = {2014.06.11}
}

@Article{Yue2010,
  Title                    = {Genome-wide investigation reveals high evolutionary rates in annual model plants.},
  Author                   = {Yue, Jia-Xing and Li, Jinpeng and Wang, Dan and Araki, Hitoshi and Tian, Dacheng and Yang, Sihai},
  Journal                  = {BMC Plant Biol},
  Year                     = {2010},
  Pages                    = {242},
  Volume                   = {10},

  Abstract                 = {Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials.According to the cross-comparisons among the four species, 74-82\% of the nuclear genes and 71-97\% of the chloroplast genes suggested 
higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level.The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those associated with 
annual/perennial life history. Although we acknowledge current limitations of this kind of study, mainly due to a small sample size available and a distant taxonomic relationship of the model organisms, our results indicate that the genome-wide survey is a promising approach toward further understanding of the mechanism determining the molecular evolutionary rate at the genomic level.},
  Institution              = {State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093, Nanjing, PR China.},
  Keywords                 = {Arabidopsis, genetics; Cell Nucleus, genetics; Chloroplasts, genetics; DNA, Chloroplast, genetics; Evolution, Molecular; Genome, Plant, genetics; Medicago truncatula, genetics; Nuclear Proteins, genetics; Phylogeny; Plant Proteins, genetics; Plants, classification/genetics; Populus, genetics; Vitis, genetics},
  Medline-pst              = {epublish},
  Owner                    = {ranjan},
  Pii                      = {1471-2229-10-242},
  Pmid                     = {21062446},
  Timestamp                = {2012.09.10}
}

@Article{Yue1995,
  Title                    = {A test of lattice protein folding algorithms.},
  Author                   = {K. Yue and K. M. Fiebig and P. D. Thomas and H. S. Chan and E. I. Shakhnovich and K. A. Dill},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {1995},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {325--329},
  Volume                   = {92},

  Abstract                 = {We report a blind test of lattice-model-based search strategies for finding global minima of model protein chains. One of us (E.I.S.) selected 10 compact conformations of 48-mer chains on the three-dimensional cubic lattice and used their inverse folding algorithm to design HP (H, hydrophobic; P, polar) sequences that should fold to those "target" structures. The sequences, but not the structures, were sent to the UCSF group (K.Y., K.M.F., P.D.T., H.S.C., and K.A.D.), who used two methods to attempt to find the globally optimal conformations: "hydrophobic zippers" and a constraint-based hydrophobic core construction (CHCC) method. The CHCC method found global minima in all cases, and the hydrophobic zippers method found global minima in some cases, in minutes to hours on workstations. In 9 out of 10 sequences, the CHCC method found lower energy conformations than the 48-mers were designed to fold to. Thus the search strategies succeed for the HP model but the design strategy 
does not. For every sequence the global energy minimum was found to have multiple degeneracy with 10(3) to 10(6) conformations. We discuss the implications of these results for (i) searching conformational spaces of simple models of proteins and (ii) how these simple models relate to proteins.},
  File                     = {:/home/ranjan/research/jabref/pdfs/Yue1995.pdf:PDF},
  Institution              = {Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204.},
  Keywords                 = {Algorithms; Amino Acid Sequence; Humans; Models, Molecular; Molecular Sequence Data; Protein Conformation; Protein Folding; Proteins, chemistry; Reproducibility of Results},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {7816842},
  Timestamp                = {2011.11.28}
}

@Article{Zaher2009,
  Title                    = {Quality control by the ribosome following peptide bond formation.},
  Author                   = {Zaher, Hani S. and Green, Rachel},
  Journal                  = {Nature},
  Year                     = {2009},

  Month                    = {Jan},
  Number                   = {7226},
  Pages                    = {161--166},
  Volume                   = {457},

  Abstract                 = {The overall fidelity of protein synthesis has been thought to rely on the combined accuracy of two basic processes: the aminoacylation of transfer RNAs with their cognate amino acid by the aminoacyl-tRNA synthetases, and the selection of cognate aminoacyl-tRNAs by the ribosome in cooperation with the GTPase elongation factor EF-Tu. These two processes, which together ensure the specific acceptance of a correctly charged cognate tRNA into the aminoacyl (A) site, operate before peptide bond formation. Here we report the identification of an additional mechanism that contributes to high fidelity protein synthesis after peptidyl transfer, using a well-defined in vitro bacterial translation system. In this retrospective quality control step, the incorporation of an amino acid from a non-cognate tRNA into the growing polypeptide chain leads to a general loss of specificity in the A site of the ribosome, and thus to a propagation of errors that results in abortive termination of 
protein synthesis.},
  Institution              = {Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.},
  Keywords                 = {Aminoacylation; Anticodon, genetics; Base Pair Mismatch, genetics; Biocatalysis; Codon, genetics; Escherichia coli Proteins, metabolism; Escherichia coli, enzymology/genetics/metabolism; Peptide Chain Termination, Translational; Peptide Termination Factors, metabolism; Protein Biosynthesis; RNA, Transfer, genetics/metabolism; Ribosomes, chemistry/genetics/metabolism; Substrate Specificity},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nature07582},
  Pmid                     = {19092806},
  Timestamp                = {2012.04.06}
}

@Article{Zahnle1990,
  Title                    = {Comet dust as a source of amino acids at the Cretaceous/Tertiary boundary.},
  Author                   = {K. Zahnle and D. Grinspoon},
  Journal                  = {Nature},
  Year                     = {1990},

  Month                    = {Nov},
  Number                   = {6297},
  Pages                    = {157--160},
  Volume                   = {348},

  Abstract                 = {Large amounts of apparently extraterrestrial amino acids have been detected recently in rocks at the Cretaceous/Tertiary (K/T) boundary at Stevns Klint, Denmark. The amino acids were found a few tens of centimetres above and below the boundary layer, but were absent in the boundary clay itself. If one supposes that these compounds were carried to the Earth by the giant meteorite thought to have impacted at the end of the Cretaceous, some puzzling questions are raised: why weren't the amino acids incinerated in the impact, and why are they not present in the boundary clay itself? Here we suggest that the amino acids were actually deposited with the dust from a giant comet trapped in the inner Solar System, a fragment of which comprised the K/T impactor. Amino acids or their precursors in the comet dust would have been swept up by the Earth both before and after the impact, but any conveyed by the impactor itself would have been destroyed. The observed amino acid layers would thus 
have been deposited without an impact.},
  File                     = {Zahnle1990.pdf:pdfs/Zahnle1990.pdf:PDF},
  Institution              = {ARC},
  Keywords                 = {Aldehydes, analysis; Amino Acids, analysis; Biogenesis; Chemical Phenomena; Chemistry; Denmark; Dust, analysis; Earth (Planet); Geologic Sediments, chemistry; Meteoroids; Nitriles, analysis; Paleontology},
  Owner                    = {ranjan},
  Pmid                     = {11536472},
  Timestamp                = {2009.09.21}
}

@Article{Zakharov1997,
  Title                    = {[Homology and evolution of gene orders: simulation and reconstruction of the evolutionary process].},
  Author                   = {I. A. Zakharov and S. V. Nikiforov and E. V. Stepaniuk},
  Journal                  = {Genetika},
  Year                     = {1997},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {31--39},
  Volume                   = {33},

  Abstract                 = {A method to reconstruct the evolutionary history of observed gene orders from estimates of their similarity has been developed. It was shown that similarity measures accounting or not accounting for gene order in linkage groups of the compared genomes can be used for this purpose. A number of plausible variants of gene-order evolution from the common ancestral form in seven primate species were obtained.},
  Keywords                 = {Animals; Chromosome Mapping; Computer Graphics; Computer Simulation; Evolution, Molecular; Humans; Models, Genetic; Primates, genetics; Sequence Homology, Nucleic Acid},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {9162689},
  Timestamp                = {2011.09.15}
}

@Article{Zandi2005,
  Title                    = {Mechanical properties of viral capsids},
  Author                   = {Zandi, R. and Reguera, D.},
  Journal                  = PRE,
  Year                     = {2005},
  Number                   = {2},
  Pages                    = {021917},
  Volume                   = {72},

  File                     = {Zandi2005.pdf:pdfs/Zandi2005.pdf:PDF}
}

@Article{Zandi2004,
  Title                    = {Origin of icosahedral symmetry in viruses},
  Author                   = {Zandi, R. and Reguera, D. and Bruinsma, R. F. and Gelbart, W. M. and Rudnick, J.},
  Journal                  = PNAS,
  Year                     = {2004},
  Number                   = {44},
  Pages                    = {15556--15560},
  Volume                   = {101},

  File                     = {Zandi2004.pdf:pdfs/Zandi2004.pdf:PDF}
}

@Article{Zandi2006,
  Title                    = {Classical nucleation theory of virus capsids.},
  Author                   = {Zandi,R. and van der Schoot,P. and Reguera,D. and Kegel,W. and Reiss,H.},
  Journal                  = {Biophys J.},
  Year                     = {2006},
  Number                   = {6},
  Pages                    = {1939--1948},
  Volume                   = {90},

  File                     = {Zandi2006.pdf:pdfs/Zandi2006.pdf:PDF}
}

@Article{Zawadzke1993,
  Title                    = {The structure of a centrosymmetric protein crystal},
  Author                   = {Zawadzke, Laura E and Berg, Jeremy M},
  Journal                  = {Proteins: Structure, Function, and Bioinformatics},
  Year                     = {1993},
  Number                   = {3},
  Pages                    = {301--305},
  Volume                   = {16},

  Owner                    = {ranjan},
  Publisher                = {Wiley Online Library},
  Timestamp                = {2016.06.06}
}

@Article{Zeldovich2007c,
  Title                    = {Protein and DNA sequence determinants of thermophilic adaptation.},
  Author                   = {Konstantin B Zeldovich and Igor N Berezovsky and Eugene I Shakhnovich},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2007},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {e5},
  Volume                   = {3},

  Abstract                 = {There have been considerable attempts in the past to relate phenotypic trait--habitat temperature of organisms--to their genotypes, most importantly compositions of their genomes and proteomes. However, despite accumulation of anecdotal evidence, an exact and conclusive relationship between the former and the latter has been elusive. We present an exhaustive study of the relationship between amino acid composition of proteomes, nucleotide composition of DNA, and optimal growth temperature (OGT) of prokaryotes. Based on 204 complete proteomes of archaea and bacteria spanning the temperature range from -10 degrees C to 110 degrees C, we performed an exhaustive enumeration of all possible sets of amino acids and found a set of amino acids whose total fraction in a proteome is correlated, to a remarkable extent, with the OGT. The universal set is Ile, Val, Tyr, Trp, Arg, Glu, Leu (IVYWREL), and the correlation coefficient is as high as 0.93. We also found that the G + C content in 
204 complete genomes does not exhibit a significant correlation with OGT (R = -0.10). On the other hand, the fraction of A + G in coding DNA is correlated with temperature, to a considerable extent, due to codon patterns of IVYWREL amino acids. Further, we found strong and independent correlation between OGT and the frequency with which pairs of A and G nucleotides appear as nearest neighbors in genome sequences. This adaptation is achieved via codon bias. These findings present a direct link between principles of proteins structure and stability and evolutionary mechanisms of thermophylic adaptation. On the nucleotide level, the analysis provides an example of how nature utilizes codon bias for evolutionary adaptation to extreme conditions. Together these results provide a complete picture of how compositions of proteomes and genomes in prokaryotes adjust to the extreme conditions of the environment.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America.},
  Keywords                 = {Adaptation, Physiological, genetics; Amino Acid Sequence; Archaea, genetics; Bacterial Proteins, genetics; Chromosome Mapping; Conserved Sequence; DNA, chemistry/genetics; Evolution, Molecular; Molecular Sequence Data; Proteome, genetics; Sequence Analysis, DNA; Sequence Analysis, Protein; Sequence Homology; Temperature},
  Owner                    = {ranjan},
  Pii                      = {06-PLCB-RA-0266R2},
  Pmid                     = {17222055},
  Timestamp                = {2009.12.05}
}

@Article{Zeldovich2006,
  Title                    = {Physical origins of protein superfamilies.},
  Author                   = {Konstantin B Zeldovich and Igor N Berezovsky and Eugene I Shakhnovich},
  Journal                  = {J Mol Biol},
  Year                     = {2006},

  Month                    = {Apr},
  Number                   = {4},
  Pages                    = {1335--1343},
  Volume                   = {357},

  Abstract                 = {In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using a standard exact three-dimensional lattice model we evolve sequences starting from random ones and determine the exact native structure after each mutation. Acceptance of mutations is biased to select for stable proteins. We found that certain structures, "wonderfolds", are independently discovered numerous times as native states of stable proteins in many unrelated runs of selection. The strong dependence of lattice fold usage on the structural determinant of designability quantitatively reproduces uneven fold usage in natural proteins. Diversity of sequences that fold into wonderfold structures gives rise to superfamilies, i.e. sets of dissimilar sequences that fold into the same or very similar structures. The present work establishes a model of pre-biotic structure selection, which identifies dominant structural patterns 
emerging upon optimization of proteins for survival in a hot environment. Convergently discovered pre-biotic initial superfamilies with wonderfold structures could have served as a seed for subsequent biological evolution involving gene duplications and divergence.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.},
  Keywords                 = {Amino Acid Sequence; Computer Simulation; Evolution, Molecular; Models, Molecular; Mutation; Protein Conformation; Protein Folding; Proteins, chemistry/genetics/metabolism},
  Owner                    = {ranjan},
  Pii                      = {S0022-2836(06)00121-5},
  Pmid                     = {16483605},
  Timestamp                = {2009.12.05}
}

@Article{Konstantin2007,
  Title                    = {A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.},
  Author                   = {Konstantin B Zeldovich and Peiqiu Chen and Boris E Shakhnovich and Eugene I Shakhnovich},
  Journal                  = {PLoS Comput Biol},
  Year                     = {2007},

  Month                    = {Jul},
  Number                   = {7},
  Pages                    = {e139},
  Volume                   = {3},

  Abstract                 = {In this work we develop a microscopic physical model of early evolution where phenotype--organism life expectancy--is directly related to genotype--the stability of its proteins in their native conformations-which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the "Big Bang" scenario whereby exponential population growth ensues as soon as favorable sequence-structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary timescales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and 
superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species--subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution.},
  File                     = {Konstantin2007.pdf:pdfs/Konstantin2007.pdf:PDF},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.},
  Keywords                 = {Animals; Chronobiology Phenomena, genetics; Computer Simulation; Databases, Protein; Evolution; Genome, physiology; Humans; Life Expectancy; Models, Genetic; Multigene Family, physiology; Mutation, physiology; Population Growth; Protein Conformation; Protein Folding; Proteins, classification/genetics; Selection (Genetics); Sequence Alignment; Sequence Analysis, Protein; Sequence Homology, Amino Acid; Stochastic Processes; Structure-Activity Relationship},
  Owner                    = {ranjan},
  Pii                      = {07-PLCB-RA-0181},
  Pmid                     = {17630830},
  Timestamp                = {2009.12.05}
}

@Article{Zeldovich2007,
  Title                    = {Protein stability imposes limits on organism complexity and speed of molecular evolution.},
  Author                   = {Konstantin B Zeldovich and Peiqiu Chen and Eugene I Shakhnovich},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2007},

  Month                    = {Oct},
  Number                   = {41},
  Pages                    = {16152--16157},
  Volume                   = {104},

  Abstract                 = {Classical population genetics a priori assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a model where fitness can be inferred from physical properties of proteins under a physiological assumption that loss of stability of any protein encoded by an essential gene confers a lethal phenotype. Accumulation of mutations in organisms containing Gamma genes can then be represented as diffusion within the Gamma-dimensional hypercube with adsorbing boundaries determined, in each dimension, by loss of a protein's stability and, at higher stability, by lack of protein sequences. Solving the diffusion equation whose parameters are derived from the data on point mutations in proteins, we determine a universal distribution of protein stabilities, in agreement with existing data. The theory provides a fundamental relation between mutation rate, maximal genome size, and thermodynamic 
response of proteins to point mutations. It establishes a universal speed limit on rate of molecular evolution by predicting that populations go extinct (via lethal mutagenesis) when mutation rate exceeds approximately six mutations per essential part of genome per replication for mesophilic organisms and one to two mutations per genome per replication for thermophilic ones. Several RNA viruses function close to the evolutionary speed limit, whereas error correction mechanisms used by DNA viruses and nonmutant strains of bacteria featuring various genome lengths and mutation rates have brought these organisms universally approximately 1,000-fold below the natural speed limit.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.},
  Keywords                 = {Biophysical Phenomena; Biophysics; Drug Stability; Evolution, Molecular; Models, Biological; Mutation; Proteins, chemistry/genetics/metabolism; Thermodynamics},
  Owner                    = {ranjan},
  Pii                      = {0705366104},
  Pmid                     = {17913881},
  Timestamp                = {2009.12.05}
}

@Article{Zeldovich2008,
  Title                    = {Understanding protein evolution: from protein physics to Darwinian selection.},
  Author                   = {Konstantin B Zeldovich and Eugene I Shakhnovich},
  Journal                  = {Annu Rev Phys Chem},
  Year                     = {2008},
  Pages                    = {105--127},
  Volume                   = {59},

  Abstract                 = {Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically 
relevant assumptions.},
  Institution              = {Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA. kzeldov@fas.harvard.edu},
  Keywords                 = {Biophysical Phenomena; Biophysics; Evolution, Molecular; Models, Biological; Protein Conformation; Proteins, chemistry/genetics/metabolism; Selection (Genetics)},
  Owner                    = {ranjan},
  Pmid                     = {17937598},
  Timestamp                = {2009.12.05}
}

@Article{Zhang2014,
  Title                    = {PEG-stabilized bilayer nanodisks as carriers for doxorubicin delivery},
  Author                   = {Zhang, Wenping and Sun, Jin and Liu, Yan and Tao, Mengying and Ai, Xiaoyu and Su, Xiaonan and Cai, Cuifang and Tang, Yilin and Feng, Zhi and Yan, Xiaodan and others},
  Journal                  = {Molecular pharmaceutics},
  Year                     = {2014},
  Number                   = {10},
  Pages                    = {3279--3290},
  Volume                   = {11},

  Owner                    = {ranjan},
  Publisher                = {ACS Publications},
  Timestamp                = {2015.04.04}
}

@Article{Zhang2006,
  Title                    = {On the origin and highly likely completeness of single-domain protein structures.},
  Author                   = {Yang Zhang and Isaac A Hubner and Adrian K Arakaki and Eugene Shakhnovich and Jeffrey Skolnick},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2006},

  Month                    = {Feb},
  Number                   = {8},
  Pages                    = {2605--2610},
  Volume                   = {103},

  Abstract                 = {The size and origin of the protein fold universe is of fundamental and practical importance. Analyzing randomly generated, compact sticky homopolypeptide conformations constructed in generic simplified and all-atom protein models, all have similar folds in the library of solved structures, the Protein Data Bank, and conversely, all compact, single-domain protein structures in the Protein Data Bank have structural analogues in the compact model set. Thus, both sets are highly likely complete, with the protein fold universe arising from compact conformations of hydrogen-bonded, secondary structures. Because side chains are represented by their Cbeta atoms, these results also suggest that the observed protein folds are insensitive to the details of side-chain packing. Sequence specificity enters both in fine-tuning the structure and thermodynamically stabilizing a given fold with respect to the set of alternatives. Scanning the models against a three-dimensional active-site library,
 close geometric matches are frequently found. Thus, the presence of active-site-like geometries also seems to be a consequence of the packing of compact, secondary structural elements. These results have significant implications for the evolution of protein structure and function.},
  Institution              = {Center of Excellence in Bioinformatics, University at Buffalo, State University of New York, 901 Washington Street, Buffalo, NY 14203, USA.},
  Keywords                 = {Animals; Binding Sites; Databases, Protein; Evolution, Molecular; Humans; Models, Molecular; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins, chemistry},
  Owner                    = {ranjan},
  Pii                      = {0509379103},
  Pmid                     = {16478803},
  Timestamp                = {2009.12.05}
}

@Article{Zhang2004,
  Title                    = {Conformational changes of the flavivirus E glycoprotein},
  Author                   = {Zhang, Y. and Zhang, W. and Ogata, S. and Clements, D. and Strauss, J.H. and Baker, T.S. and Kuhn, R.J. and Rossmann, M.G.},
  Journal                  = {Structure.},
  Year                     = {2004},
  Number                   = {9},
  Pages                    = {1607--1618},
  Volume                   = {12},

  File                     = {Zhang2004.pdf:pdfs/Zhang2004.pdf:PDF}
}

@Article{Zhao2007,
  Title                    = {GC content variability of eubacteria is governed by the pol III alpha subunit.},
  Author                   = {Zhao, Xiaoqian and Zhang, Zhang and Yan, Jiangwei and Yu, Jun},
  Journal                  = {Biochem Biophys Res Commun},
  Year                     = {2007},

  Month                    = {Apr},
  Number                   = {1},
  Pages                    = {20--25},
  Volume                   = {356},

  Abstract                 = {Eubacterial genomes have highly variable GC content (0.17-0.75) and the primary mechanism of such variability remains unknown. The place to look for is what actually catalyzes the synthesis of DNA, where DNA polymerase III is at the center stage, particularly one of its 10 subunits--the alpha subunit. According to the dimeric combination of alpha subunits, GC contents of eubacterial genomes were partitioned into three groups with distinct GC content variation spectra: dnaE1 (full-spectrum), dnaE2/dnaE1 (high-GC), and polC/dnaE3 (low-GC). Therefore, genomic GC content variability is believed to be governed primarily by the alpha subunit grouping of DNA polymerase III; it is of essence in genome composition analysis to take full account of such a grouping principle. Since horizontal gene transfer is very frequent among bacterial genomes, exceptions of the grouping scheme, a few percents of the total, are readily identifiable and should be excluded from in-depth analyses on 
nucleotide compositions.},
  Institution              = {Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China.},
  Keywords                 = {Bacteria, classification/enzymology/genetics; Base Composition, genetics; DNA Polymerase III, genetics; Databases, Nucleic Acid; Genetic Variation; Phylogeny},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0006-291X(07)00337-3},
  Pmid                     = {17336933},
  Timestamp                = {2012.09.26}
}

@Article{Zhao2005,
  Title                    = {Exchange-correlation functional with broad accuracy for metallic and nonmetallic compounds, kinetics, and noncovalent interactions},
  Author                   = {Zhao, Yan and Schultz, Nathan E and Truhlar, DG},
  Journal                  = {The Journal of chemical physics},
  Year                     = {2005},
  Number                   = {16},
  Pages                    = {161103},
  Volume                   = {123},

  Owner                    = {ranjan},
  Publisher                = {AIP Publishing},
  Timestamp                = {2014.07.23}
}

@Article{Zheng2008,
  Title                    = {Image reconstruction in electron microscopy},
  Author                   = {Zheng,Y. and Lee,S. and Doerschuk,P.C.},
  Journal                  = {Proc. SPIE},
  Year                     = {2008},
  Pages                    = {70760G},
  Volume                   = {7076},

  File                     = {Zheng2008.pdf:pdfs/Zheng2008.pdf:PDF},
  Owner                    = {ranjan},
  Timestamp                = {2009.06.17}
}

@Article{Zhou2001,
  Title                    = {Stabilization of proteins in confined spaces.},
  Author                   = {H. X. Zhou and K. A. Dill},
  Journal                  = {Biochemistry},
  Year                     = {2001},

  Month                    = {Sep},
  Number                   = {38},
  Pages                    = {11289--11293},
  Volume                   = {40},

  Abstract                 = {We present theory showing that confining a protein to a small inert space (a "cage") should stabilize the protein against reversible unfolding. Examples of such spaces might include the pores within chromatography columns, the Anfinsen cage in chaperonins, the interiors of ribosomes, or regions of steric occlusion inside cells. Confinement eliminates some expanded configurations of the unfolded chain, shifting the equilibrium from the unfolded state toward the native state. The partition coefficient for a protein in a confined space is predicted to decrease significantly when the solvent is changed from native to denaturing conditions. Small cages are predicted to increase the stability of the native state by as much as 15 kcal/mol. Confinement may also increase the rates of protein or RNA folding.},
  Institution              = {Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, USA. hxzhou@einstein.drexel.edu},
  Keywords                 = {Chaperonins, chemistry; Drug Stability; Models, Molecular; Models, Theoretical; Peptides, chemistry; Protein Conformation; Protein Folding; Proteins, chemistry; RNA, chemistry; Ribosomes, ultrastructure; Thermodynamics},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {bi0155504},
  Pmid                     = {11560476},
  Timestamp                = {2011.11.03}
}

@Article{Zhou2012,
  Title                    = {Intrinsic disorder: signaling via highly specific but short-lived association.},
  Author                   = {Zhou, Huan-Xiang},
  Journal                  = {Trends Biochem Sci},
  Year                     = {2012},

  Month                    = {Feb},
  Number                   = {2},
  Pages                    = {43--48},
  Volume                   = {37},

  Abstract                 = {Association between signaling proteins and their cellular targets is generally thought to be highly specific (implicating a high association constant, K(a)) and, at the same time, transient or short-lived (corresponding to a high dissociation rate constant, k(d)). However, a combination of high K(a) and high k(d) would lead to a high association rate constant (k(a) = K(a)k(d)), which poses a problem because there is a limit to which k(a) can be increased, set by the diffusional approach to form the complex. In this Opinion article, I propose that having the signaling protein disordered before binding to the target provides a way out of this quandary. The intrinsic disorder of the signaling protein would decrease K(a) without sacrificing the specificity of the complex, and thus would allow k(d) to be increased to a range appropriate for signaling.},
  Doi                      = {10.1016/j.tibs.2011.11.002},
  Institution              = {Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA. hzhou4@fsu.edu},
  Keywords                 = {Binding Sites; Cell Communication; Kinetics; Proteins, chemistry/metabolism; Signal Transduction},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0968-0004(11)00185-X},
  Pmid                     = {22154231},
  Timestamp                = {2013.12.06}
}

@Article{Zhou2010,
  Title                    = {From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions.},
  Author                   = {Zhou, Huan-Xiang},
  Journal                  = {Biophys J},
  Year                     = {2010},

  Month                    = {Mar},
  Number                   = {6},
  Pages                    = {L15--L17},
  Volume                   = {98},

  Abstract                 = {In receptor-ligand binding, a question that generated considerable interest is whether the mechanism is induced fit or conformational selection. This question is addressed here by a solvable model, in which a receptor undergoes transitions between active and inactive forms. The inactive form is favored while unbound but the active form is favored while a ligand is loosely bound. As the active-inactive transition rates increase, the binding mechanism gradually shifts from conformational selection to induced fit. The timescale of conformational transitions thus plays a crucial role in controlling binding mechanisms.},
  Doi                      = {10.1016/j.bpj.2009.11.029},
  Institution              = {Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA. hzhou4@fsu.edu},
  Keywords                 = {Binding Sites; Computer Simulation; Ligands; Models, Chemical; Models, Molecular; Protein Binding; Protein Conformation; Receptors, Cell Surface, chemistry/ultrastructure},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {S0006-3495(09)01758-5},
  Pmid                     = {20303846},
  Timestamp                = {2014.02.09}
}

@Article{Zhu2013,
  Title                    = {Human pluripotent stem cells: an emerging model in developmental biology},
  Author                   = {Zhu, Zengrong and Huangfu, Danwei},
  Journal                  = {Development},
  Year                     = {2013},
  Number                   = {4},
  Pages                    = {705--717},
  Volume                   = {140},

  Owner                    = {ranjan},
  Publisher                = {The Company of Biologists Limited},
  Timestamp                = {2013.07.01}
}

@Article{Zimmermann2006,
  Title                    = {Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics.},
  Author                   = {J?rg Zimmermann and Erin L Oakman and Ian F Thorpe and Xinghua Shi and Paul Abbyad and Charles L {Brooks III} and Steven G Boxer and Floyd E Romesberg},
  Journal                  = {Proc Natl Acad Sci U S A},
  Year                     = {2006},

  Month                    = {Sep},
  Number                   = {37},
  Pages                    = {13722--13727},
  Volume                   = {103},

  Abstract                 = {The evolution of proteins with novel function is thought to start from precursor proteins that are conformationally heterogeneous. The corresponding genes may be duplicated and then mutated to select and optimize a specific conformation. However, testing this idea has been difficult because of the challenge of quantifying protein flexibility and conformational heterogeneity as a function of evolution. Here, we report the characterization of protein heterogeneity and dynamics as a function of evolution for the antifluorescein antibody 4-4-20. Using nonlinear laser spectroscopy, surface plasmon resonance, and molecular dynamics simulations, we demonstrate that evolution localized the Ab-combining site from a heterogeneous ensemble of conformations to a single conformation by introducing mutations that act cooperatively and over significant distances to rigidify the protein. This study demonstrates how protein dynamics may be tailored by evolution and has important implications for 
our understanding of how novel protein functions are evolved.},
  Institution              = {Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.},
  Keywords                 = {Animals; Antibodies, chemistry/genetics; Evolution, Molecular; Fluorescein; Humans; Immunoglobulin Fab Fragments, chemistry/genetics; Mutation; Protein Conformation; Proteins, chemistry/genetics; Surface Plasmon Resonance},
  Owner                    = {ranjan},
  Pii                      = {0603282103},
  Pmid                     = {16954202},
  Timestamp                = {2009.12.05}
}

@Article{Zlotnick2000,
  Title                    = {Mechanism of capsid assembly for an icosahedral plant virus.},
  Author                   = {Zlotnick,A. and Aldrich,R. and Johnson,J.M. and Ceres,P. and Young,M.J.},
  Journal                  = {Virology.},
  Year                     = {2000},
  Number                   = {2},
  Pages                    = {450--456},
  Volume                   = {277},

  File                     = {Zlotnick2000.pdf:pdfs/Zlotnick2000.pdf:PDF}
}

@Article{Zubieta2005,
  Title                    = {The structure of the human adenovirus 2 penton.},
  Author                   = {Zubieta, C. and Schoehn, G. and Chroboczek, J. and Cusack, S.},
  Journal                  = {Mol Cell.},
  Year                     = {2005},
  Number                   = {1},
  Pages                    = {121-135},
  Volume                   = {17},

  File                     = {Zubieta2005.pdf:pdfs/Zubieta2005.pdf:PDF}
}

@Article{Zuckerkandl1965,
  Title                    = {Molecules as documents of evolutionary history.},
  Author                   = {E. Zuckerkandl and L. Pauling},
  Journal                  = {J Theor Biol},
  Year                     = {1965},

  Month                    = {Mar},
  Number                   = {2},
  Pages                    = {357--366},
  Volume                   = {8},

  Keywords                 = {Amino Acid Sequence; Biological Evolution; Genes; Genetic Code; Macromolecular Substances; Nucleic Acids; RNA, Messenger},
  Owner                    = {ranjan},
  Pii                      = {0022-5193(65)90083-4},
  Pmid                     = {5876245},
  Timestamp                = {2011.04.27}
}

@Article{Zuckerkandl1965a,
  Title                    = {Evolutionary divergence and convergence in proteins},
  Author                   = {Zuckerkandl, Emile and Pauling, Linus},
  Journal                  = {Evolving genes and proteins},
  Year                     = {1965},
  Pages                    = {97--166},
  Volume                   = {97},

  Owner                    = {ranjan},
  Timestamp                = {2013.12.01}
}

@InBook{Zuckerkandl1962,
  Title                    = {Molecular disease, evolution, and genetic heterogeneity},
  Author                   = {Zuckerkandl, E. and Pauling, L. B.},
  Editor                   = {Kasha, M. and Pullman, B.},
  Pages                    = {189--225},
  Publisher                = {Academic Press},
  Year                     = {1962},

  Address                  = {New York},

  Owner                    = {ranjan},
  Timestamp                = {2010.02.07}
}

@Article{Zuckermann2009,
  Title                    = {Peptoids as potential therapeutics.},
  Author                   = {Zuckermann, Ronald N. and Kodadek, Thomas},
  Journal                  = {Curr Opin Mol Ther},
  Year                     = {2009},

  Month                    = {Jun},
  Number                   = {3},
  Pages                    = {299--307},
  Volume                   = {11},

  Abstract                 = {Peptoids are oligomers of N-substituted glycine units. These molecules are almost perfectly suited for combinatorial approaches to drug discovery because large libraries can be synthesized easily from readily available primary amines. Moreover, major advances in screening methodology have allowed peptoid libraries of hundreds of thousands of compounds to be mined inexpensively and quickly for highly specific protein-binding molecules. These advances and the potential utility of peptoids as pharmacological agents are reviewed.},
  Institution              = {Lawrence Berkeley National Laboratory, Biological Nanostructures Facility, The Molecular Foundry, Berkeley, CA 94720, USA. RNZuckermann@lbl.gov},
  Keywords                 = {Animals; Drug Discovery; Drug Evaluation, Preclinical; Drug Industry; Humans; Peptoids, chemical synthesis/chemistry/therapeutic use},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pmid                     = {19479663},
  Timestamp                = {2012.07.15}
}

@Book{Darwin1887,
  Title                    = {The life and letters of Charles Darwin, including an autobiographical chapter},
  Editor                   = {Darwin, Francis},
  Publisher                = {London: John Murray},
  Year                     = {1887},
  Volume                   = {3},

  Owner                    = {ranjan},
  Timestamp                = {2012.04.09}
}

@Electronic{NPROddEven,
  Title                    = {Romney, Obama Have Parallel Points On The Economy},
  HowPublished             = {NPR.org Radio Transcript (October 03 2012; 3:00 PM)},
  Month                    = {October},

  Owner                    = {ranjan},
  Timestamp                = {2014.01.15}
}

@Article{ProteomesHypothesisFootnote1,
  Title                    = {Note that a critical distinction exists between the extent towards which a species has deviated from the last common ancestor and the genetic diversity available to a species. The former metric is sourced from taxonomy and measures new features distinct from the last common ancestor (e.g., the presence of nuclei, specialized proteins, limbs, etc), while the latter is a measure of the allelic diversity present within the features of a species. More on this discussion is available in \cite{Mannige2012}.},

  Owner                    = {ranjan},
  Timestamp                = {2014.02.24}
}

@Article{ProteomesHypothesisFootnote2,
  Title                    = {Note that affinity maturation is only used as an example to indicate the importance of a transition from a dynamic to rigid state; the actual {\it mode} of maturation is far too specialized to be generalized as a relevant mechanism of evolution.},

  Owner                    = {ranjan},
  Timestamp                = {2014.02.25}
}

@Article{ProteomesReviewFootnote1,
  Title                    = {Kendrew's structure\cite{Kendrew1958} predated the Protein Databank\cite{Berman2000}; however, Watson and Kendrew eventually deposited into the PDB a {\it refined} version of the original structure in 1973; PDB ID: \href{http://www.pdb.org/pdb/explore/explore.do?pdbId=1MBN}{1MBN}.},

  Owner                    = {ranjan},
  Timestamp                = {2014.02.08}
}

@Article{ProteomesReviewFootnote2,
  Title                    = {For example, the first decade of structure deposition in the PDB--the 1970's--witnessed only one of 92 deposited protein chains (PDB ID \href{http://www.pdb.org/pdb/explore/explore.do?pdbId=1CHG}{1CHG}, chain A) that displayed a substantial number of residues ($>$5\%) with missing backbone coordinates.},

  Owner                    = {ranjan},
  Timestamp                = {2014.02.08}
}

@Article{ProteomesReviewFootnote3,
  Title                    = {From Uversky {\it{et al.}}'s findings, a protein with high net charge magnitude ($R$) {\it could} remain folded if it were countered by high hydrophobicity ($H$; on a Kyte-Doolittle scale normalized to range between 0 and 1\cite{Uversky2000a}); accordingly, the remarkable boundary line on the $H$-$R$ landscape that distinguishes folding vs. disordered proteins was reported\cite{Uversky2000a} to be: \newline$\langle R \rangle = 2.785 \langle H \rangle - 1.151$.},

  Owner                    = {ranjan},
  Timestamp                = {2014.02.08}
}

@Article{ProteomesReviewFootnote4,
  Title                    = {Pauling {\it et al}.,\cite{Pauling1951} adhered to basic but still relatively new chemical principles such as planarity of the amide bond within each amino acid and linear hydrogen bonding rules (notions that were omitted in a previously failed attempt a year earlier by luminaries Bragg, Kendrew, and Perutz\cite{Bragg1950}).},

  Owner                    = {ranjan},
  Timestamp                = {2014.02.08}
}

@Article{NatureNanotechnologyEditorial2009,
  Title                    = {'Plenty of room' revisited.},
  Journal                  = {Nat Nanotechnol},
  Year                     = {2009},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {781},
  Volume                   = {4},

  Doi                      = {10.1038/nnano.2009.356},
  Medline-pst              = {ppublish},
  Owner                    = {ranjan},
  Pii                      = {nnano.2009.356},
  Pmid                     = {19966817},
  Timestamp                = {2014.04.19}
}

@Article{Shannon1948,
  author  = {Shannon, Claude Elwood},
  title   = {A mathematical theory of communication},
  year    = {1948},
  volume  = {27},
  number  = {4},
  pages   = {623--666},
  journal = {Bell System Technical Journal},
}

@InProceedings{Kostic2011,
  author    = {Kostic, Milivoje M},
  title     = {Revisiting the second law of energy degradation and entropy generation: From Sadi Carnot's ingenious reasoning to Holistic generalization},
  booktitle = {AIP Conference Proceedings-American Institute of Physics},
  year      = {2011},
  volume    = {1411},
  number    = {1},
  pages     = {327},
}

@Article{Carnot1824,
  author  = {Carnot, Sadi},
  title   = {Reflections on the motive power of fire, and on machines fitted to develop that power},
  year    = {1824},
  journal = {Paris: Bachelier},
}

@InCollection{Jaynes1965,
  author  = {Jaynes, E. T.},
  title   = {Gibbs vs Boltzmann Entropies},
  year    = {1965},
  volume  = {33},
  number  = {4},
  pages   = {391--398},
  journal = {American Journal of Physics},
}

@Article{Rothstein1951,
  author  = {Rothstein, Jerome},
  title   = {INFORMATION AND ENTROPY},
  year    = {1951},
  volume  = {114},
  pages   = {171--175},
  journal = {Science},
}

@Article{Gibbs1902,
  author  = {Gibbs, J Willard},
  title   = {Elementary Principles in Statistical Mechanics (Scribner},
  year    = {1902},
  journal = {New York},
}

@Article{Chakrabarti2007,
  author  = {Chakrabarti, CG and Chakrabarty, Indranil},
  title   = {Boltzmann entropy: probability and information},
  year    = {2007},
  journal = {arXiv preprint arXiv:0705.2850},
}

@Misc{Boltzmann1964,
  author    = {Boltzmann, L},
  title     = {Lectures on gas theory, translated by SG Brush, University of Cal},
  year      = {1964},
  publisher = {Press},
}

@Book{Ben-Naim2008,
  author    = {Ben-Naim, Arieh},
  title     = {A Farewell to Entropy: Statistical Thermodynamics Based on Information: S},
  year      = {2008},
  publisher = {World Scientific},
}

@Article{Kostic2014,
  author    = {Kostic, Milivoje M},
  title     = {The elusive nature of entropy and its physical meaning},
  year      = {2014},
  volume    = {16},
  number    = {2},
  pages     = {953--967},
  journal   = {Entropy},
  publisher = {Multidisciplinary Digital Publishing Institute},
}

@Book{Ben-Naim2008b,
  author    = {Ben-N{\=a}ʿ{\^\i}m, Ary{\=e}},
  title     = {Entropy demystified},
  year      = {2008},
  publisher = {World Scientific},
}

@Article{Ben-Naim2007,
  author    = {Ben-Naim, Arieh},
  title     = {On the so-called Gibbs paradox, and on the real paradox},
  year      = {2007},
  volume    = {9},
  number    = {3},
  pages     = {132--136},
  journal   = {Entropy},
  publisher = {Molecular Diversity Preservation International},
}

@Article{Ben-Naim2011,
  author    = {Ben-Naim, Arieh},
  title     = {Entropy: Order or information},
  year      = {2011},
  volume    = {88},
  number    = {5},
  pages     = {594--596},
  journal   = {Journal of Chemical Education},
  publisher = {ACS Publications},
}

@Article{Lynch2015,
  author    = {Lynch, Michael and Marinov, Georgi K},
  title     = {The bioenergetic costs of a gene},
  year      = {2015},
  volume    = {112},
  number    = {51},
  pages     = {15690--15695},
  journal   = {Proceedings of the National Academy of Sciences},
  publisher = {National Acad Sciences},
}

@Article{Lynch2000,
  author    = {Lynch, Michael and Conery, John S},
  title     = {The evolutionary fate and consequences of duplicate genes},
  year      = {2000},
  volume    = {290},
  number    = {5494},
  pages     = {1151--1155},
  journal   = {Science},
  publisher = {American Association for the Advancement of Science},
}

@Article{Wei2015,
  author  = {Wei, Bryan and Vhudzijena, Michelle K and Robaszewski, Joanna and Yin, Peng},
  title   = {Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles},
  year    = {2015},
  number  = {99},
  pages   = {e52486--e52486},
  journal = {JoVE (Journal of Visualized Experiments)},
}

@Article{SantaLuciaJr2004,
  author    = {SantaLucia Jr, John and Hicks, Donald},
  title     = {The thermodynamics of DNA structural motifs},
  year      = {2004},
  volume    = {33},
  pages     = {415--440},
  journal   = {Annu. Rev. Biophys. Biomol. Struct.},
  publisher = {Annual Reviews},
}

@Article{Zlotnick2005,
  author    = {Zlotnick, A},
  title     = {Simple models and simple analyses of virus capsid assembly},
  year      = {2005},
  volume    = {6},
  number    = {2},
  pages     = {111--114},
  journal   = {Journal of Theoretical Medicine},
  publisher = {Taylor \& Francis},
}

@Article{Planck1901,
  author    = {Planck, Max},
  title     = {Ueber das gesetz der energieverteilung im normalspectrum},
  year      = {1901},
  volume    = {309},
  number    = {3},
  pages     = {553--563},
  journal   = {Annalen der physik},
  publisher = {Wiley Online Library},
}

@Article{Kwiecinska2005,
  author    = {Kwieci{\'n}ska, Joanna I and Cieplak, Marek},
  title     = {Chirality and protein folding},
  year      = {2005},
  volume    = {17},
  number    = {18},
  pages     = {S1565},
  journal   = {Journal of Physics: Condensed Matter},
  publisher = {IOP Publishing},
}

@Article{Gruziel2013,
  author    = {Gruziel, Magdalena and Dzwolak, Wojciech and Szymczak, Piotr},
  title     = {Chirality inversions in self-assembly of fibrillar superstructures: a computational study},
  year      = {2013},
  volume    = {9},
  number    = {33},
  pages     = {8005--8013},
  journal   = {Soft Matter},
  publisher = {Royal Society of Chemistry},
}

@Article{Neal2003,
  author    = {Neal, Maureen P and Solymosi, Miklos and Wilson, Mark R and Earl, David J},
  title     = {Helical twisting power and scaled chiral indices},
  year      = {2003},
  volume    = {119},
  number    = {6},
  pages     = {3567--3573},
  journal   = {The Journal of chemical physics},
  publisher = {AIP Publishing},
}

@Article{Solymosi2002,
  author    = {Solymosi, Miklos and Low, Robert J and Grayson, Martin and Neal, Maureen P},
  title     = {A generalized scaling of a chiral index for molecules},
  year      = {2002},
  volume    = {116},
  number    = {22},
  pages     = {9875--9881},
  journal   = {The Journal of chemical physics},
  publisher = {AIP Publishing},
}

@Article{Quiocho1977,
  author    = {Quiocho, FLORANTE A and Gilliland, GARY L and Phillips, GN},
  title     = {The 2.8-A resolution structure of the L-arabinose-binding protein from Escherichia coli. Polypeptide chain folding, domain similarity, and probable location of sugar-binding site.},
  year      = {1977},
  volume    = {252},
  number    = {14},
  pages     = {5142--5149},
  journal   = {Journal of Biological Chemistry},
  publisher = {ASBMB},
}

@Article{Shaw1977,
  author    = {Shaw, Peter J and Muirhead, Hilary},
  title     = {Crystallographic structure analysis of glucose 6-phosphate isomerase at 3{\textperiodcentered} 5 {\AA} resolution},
  year      = {1977},
  volume    = {109},
  number    = {3},
  pages     = {475--485},
  journal   = {Journal of molecular biology},
  publisher = {Elsevier},
}

@Article{Schulz1974,
  author  = {Schulz, GE and Elzinga, M and Marx, F and Schirmer, RH},
  title   = {Three-dimensional structure of adenyl kinase},
  year    = {1974},
  volume  = {250},
  pages   = {120--123},
  journal = {Nature},
}

@Article{Chothia1977,
  author    = {Chothia, Cyrus and Levitt, Michael and Richardson, Douglas},
  title     = {Structure of proteins: packing of alpha-helices and pleated sheets},
  year      = {1977},
  volume    = {74},
  number    = {10},
  pages     = {4130--4134},
  journal   = {Proceedings of the National Academy of Sciences},
  publisher = {National Acad Sciences},
}

@Article{Gorske2016,
  author    = {Gorske, Benjamin C and Mumford, Emily M and Conry, Rebecca R},
  title     = {Tandem Incorporation of Enantiomeric Residues Engenders Discrete Peptoid Structures},
  year      = {2016},
  journal   = {Organic letters},
  publisher = {ACS Publications},
}

@Article{Robertson2016,
  author    = {Robertson, Ellen J and Battigelli, Alessia and Proulx, Caroline and Mannige, Ranjan V and Haxton, Thomas K and Yun, Lisa and Whitelam, Stephen and Zuckermann, Ronald N},
  title     = {Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets},
  year      = {2016},
  volume    = {49},
  number    = {3},
  pages     = {379--389},
  journal   = {Accounts of chemical research},
  publisher = {ACS Publications},
}

@Article{Moreno2011,
  author    = {Moreno, Luis F},
  title     = {Understanding Fischer Projection and Angular Line Representation Conversion},
  year      = {2011},
  volume    = {89},
  number    = {1},
  pages     = {175--176},
  journal   = {Journal of Chemical Education},
  publisher = {ACS Publications},
}

@Book{Cross2013,
  author    = {Cross, LC and Klyne, W},
  title     = {Rules for the Nomenclature of Organic Chemistry: Section E: Stereochemistry (Recommendations 1974)},
  year      = {2013},
  publisher = {Elsevier},
}

@Book{Liddell1894,
  author    = {Liddell, Henry George and Scott, Robert and Drisler, Henry},
  title     = {A greek-english lexicon},
  year      = {1894},
  publisher = {Harper \& brothers},
}

@Article{Liddell1940,
  author    = {Liddell, Henry George and Scott, Robert and Jones, Henry Stuart and others},
  title     = {A Greek-English lexicon/compiled by Henry George Liddell and Robert Scott.},
  year      = {1940},
  publisher = {Oxford: Clarendon,},
}

@Article{Miyazawa1961,
  author    = {Miyazawa, Tatsuo},
  title     = {Molecular vibrations and structure of high polymers. II. Helical parameters of infinite polymer chains as functions of bond lengths, bond angles, and internal rotation angles},
  journal   = {Journal of Polymer Science},
  year      = {1961},
  volume    = {55},
  number    = {161},
  pages     = {215--231},
  publisher = {Wiley Online Library},
}

@Article{Shimanouchi1955,
  author    = {Shimanouchi, Takehiko and Mizushima, San-ichiro},
  title     = {On the helical configuration of a polymer chain},
  journal   = {The Journal of Chemical Physics},
  year      = {1955},
  volume    = {23},
  number    = {4},
  pages     = {707--711},
  publisher = {AIP Publishing},
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@Article{Kandakov2013,
  author    = {Kandakov, AV and Ginzburg, BM},
  title     = {Construction of Myazawa's Equations for the Case of an Arbitrary Number of Junction Atoms},
  journal   = {Journal of Macromolecular Science, Part B},
  year      = {2013},
  volume    = {52},
  number    = {8},
  pages     = {1056--1063},
  publisher = {Taylor \& Francis},
}

@Article{Zacharias2013,
  author    = {Zacharias, Jan and Knapp, Ernst Walter},
  title     = {Geometry motivated alternative view on local protein backbone structures},
  journal   = {Protein Science},
  year      = {2013},
  volume    = {22},
  number    = {11},
  pages     = {1669--1674},
  publisher = {Wiley Online Library},
}

@Article{Ho2003,
  author    = {Ho, Bosco K and Thomas, Annick and Brasseur, Robert},
  title     = {Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the $\alpha$-helix},
  journal   = {Protein Science},
  year      = {2003},
  volume    = {12},
  number    = {11},
  pages     = {2508--2522},
  publisher = {Wiley Online Library},
}

@InCollection{Engh2006,
  author    = {Engh, RA and Huber, R},
  title     = {Structure quality and target parameters},
  booktitle = {International Tables for Crystallography Volume F: Crystallography of biological macromolecules},
  year      = {2006},
  publisher = {Springer},
  pages     = {382--392},
}

@Article{Engh1991,
  author    = {Engh, Richard A and Huber, Robert},
  title     = {Accurate bond and angle parameters for X-ray protein structure refinement},
  journal   = {Acta Crystallographica Section A: Foundations of Crystallography},
  year      = {1991},
  volume    = {47},
  number    = {4},
  pages     = {392--400},
  publisher = {International Union of Crystallography},
}

@Article{Nemethy1966,
  author    = {N{\'e}methy, George and Leach, SJ and Scheraga, Harold A},
  title     = {The Influence of Amino Acid Side Chains on the Free Energy of Helix-Coil Transitions1},
  journal   = {The Journal of Physical Chemistry},
  year      = {1966},
  volume    = {70},
  number    = {4},
  pages     = {998--1004},
  publisher = {ACS Publications},
}

@Article{Voelz2011,
  author    = {Voelz, Vincent A and Dill, Ken A and Chorny, Ilya},
  title     = {Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER},
  journal   = {Peptide Science},
  year      = {2011},
  volume    = {96},
  number    = {5},
  pages     = {639--650},
  publisher = {Wiley Online Library},
}

@Article{Osipov1995,
  author    = {Osipov, MA and Pickup, BT and Dunmur, DA},
  title     = {A new twist to molecular chirality: intrinsic chirality indices},
  journal   = {Molecular Physics},
  year      = {1995},
  volume    = {84},
  number    = {6},
  pages     = {1193--1206},
  publisher = {Taylor \& Francis},
}

@Article{Ferrarini1998,
  author    = {Ferrarini, Alberta and Nordio, Pier Luigi},
  title     = {On the assessment of molecular chirality},
  journal   = {Journal of the Chemical Society, Perkin Transactions 2},
  year      = {1998},
  number    = {2},
  pages     = {455--460},
  publisher = {Royal Society of Chemistry},
}

@Article{Harris1999,
  author    = {Harris, A Brooks and Kamien, Randall D and Lubensky, Thomas C},
  title     = {Molecular chirality and chiral parameters},
  journal   = {Reviews of Modern Physics},
  year      = {1999},
  volume    = {71},
  number    = {5},
  pages     = {1745},
  publisher = {APS},
}

@Article{VanDerWalt2011,
  author    = {Van Der Walt, Stefan and Colbert, S Chris and Varoquaux, Gael},
  title     = {The NumPy array: a structure for efficient numerical computation},
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