Published in Genome Res on March 01, 2005
Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution. Microbiol Mol Biol Rev (2006) 1.34
A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds. PLoS Comput Biol (2007) 1.26
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evol Biol (2008) 1.24
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. Genome Biol (2011) 1.22
MANET: tracing evolution of protein architecture in metabolic networks. BMC Bioinformatics (2006) 1.00
A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS One (2011) 0.96
Improving the precision of the structure-function relationship by considering phylogenetic context. PLoS Comput Biol (2005) 0.93
ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets. BMC Bioinformatics (2009) 0.82
In silico prediction of human pathogenicity in the γ-proteobacteria. PLoS One (2010) 0.81
Phylogenetic position of aquificales based on the whole genome sequences of six aquificales species. Int J Evol Biol (2012) 0.78
Improvisation in evolution of genes and genomes: whose structure is it anyway? Curr Opin Struct Biol (2008) 0.77
Evolution of structural shape in bacterial globin-related proteins. J Mol Evol (2006) 0.77
Divergent evolution of a structural proteome: phenomenological models. Biophys J (2006) 0.76
Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling. Evol Bioinform Online (2012) 0.75
Prokaryotic phylogenies inferred from whole-genome sequence and annotation data. Biomed Res Int (2013) 0.75
Genome-wide gene order distances support clustering the gram-positive bacteria. Front Microbiol (2015) 0.75
The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 266.90
Lateral gene transfer and the nature of bacterial innovation. Nature (2000) 20.98
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res (2003) 18.64
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol (2001) 15.97
Phylogenetic classification and the universal tree. Science (1999) 14.28
Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci U S A (1996) 7.17
Prokaryotic evolution in light of gene transfer. Mol Biol Evol (2002) 6.53
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. BMC Evol Biol (2003) 4.70
Universal trees based on large combined protein sequence data sets. Nat Genet (2001) 4.63
Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol (2001) 4.59
The structure of the protein universe and genome evolution. Nature (2002) 4.47
Evolution of the protein repertoire. Science (2003) 4.24
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet (1998) 4.10
Genome trees and the tree of life. Trends Genet (2002) 3.79
Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res (1999) 3.32
Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci U S A (2002) 2.92
SHOT: a web server for the construction of genome phylogenies. Trends Genet (2002) 2.79
Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol (1997) 2.79
A complete sequence of the T. tengcongensis genome. Genome Res (2002) 2.60
Identification of homology in protein structure classification. Nat Struct Biol (2001) 2.52
Distribution of protein folds in the three superkingdoms of life. Genome Res (1999) 2.29
The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res (1996) 2.10
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res (2000) 1.89
Ancient phylogenetic relationships. Theor Popul Biol (2002) 1.78
Phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol Biol Evol (2001) 1.77
Estimating the number of protein folds and families from complete genome data. J Mol Biol (2000) 1.71
Estimating the number of protein folds. J Mol Biol (1998) 1.33
Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol (2002) 1.29
The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J Mol Evol (2004) 1.29
Phylogenetic depth of the bacterial genera Aquifex and Thermotoga inferred from analysis of ribosomal protein, elongation factor, and RNA polymerase subunit sequences. J Mol Evol (2000) 1.12
Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion? Mol Phylogenet Evol (2002) 1.10
Proteomic traces of speciation. J Mol Biol (2004) 0.95
ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations. BMC Bioinformatics (2003) 0.94
Target practice. Nat Struct Biol (2001) 0.93
Protein evolution within a structural space. Biophys J (2003) 0.92
Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci U S A (2002) 2.92
Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci U S A (2007) 2.16
Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol (2006) 2.15
Topological determinants of protein folding. Proc Natl Acad Sci U S A (2002) 2.12
The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc Natl Acad Sci U S A (2002) 1.86
Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol (2003) 1.80
A simple physical model for scaling in protein-protein interaction networks. Proc Natl Acad Sci U S A (2005) 1.78
Physics and evolution of thermophilic adaptation. Proc Natl Acad Sci U S A (2005) 1.72
Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proc Natl Acad Sci U S A (2003) 1.67
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J Mol Biol (2002) 1.66
The folding mechanics of a knotted protein. J Mol Biol (2007) 1.64
A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proc Natl Acad Sci U S A (2011) 1.56
Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J (2002) 1.55
Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput Biol (2007) 1.51
Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Mol Syst Biol (2008) 1.50
Structural determinant of protein designability. Phys Rev Lett (2003) 1.41
All-atom ab initio folding of a diverse set of proteins. Structure (2007) 1.36
Robust protein protein interactions in crowded cellular environments. Proc Natl Acad Sci U S A (2007) 1.32
Predicting specificity-determining residues in two large eukaryotic transcription factor families. Nucleic Acids Res (2005) 1.30
A structure-based method for derivation of all-atom potentials for protein folding. Proc Natl Acad Sci U S A (2002) 1.28
Energetics of protein-DNA interactions. Nucleic Acids Res (2007) 1.26
A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds. PLoS Comput Biol (2007) 1.26
Imprint of evolution on protein structures. Proc Natl Acad Sci U S A (2004) 1.24
Universality and diversity of folding mechanics for three-helix bundle proteins. Proc Natl Acad Sci U S A (2008) 1.24
Natural selection of more designable folds: a mechanism for thermophilic adaptation. Proc Natl Acad Sci U S A (2003) 1.24
Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci U S A (2006) 1.19
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. J Mol Biol (2005) 1.18
Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations. Proc Natl Acad Sci U S A (2012) 1.18
Commitment and nucleation in the protein G transition state. J Mol Biol (2004) 1.18
Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness. Mol Cell (2012) 1.16
SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. J Med Chem (2002) 1.14
Lethal mutagenesis in viruses and bacteria. Genetics (2009) 1.11
Entropic stabilization of proteins and its proteomic consequences. PLoS Comput Biol (2005) 1.11
All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples. J Am Chem Soc (2009) 1.10
Nucleation and the transition state of the SH3 domain. J Mol Biol (2005) 1.10
High-resolution protein folding with a transferable potential. Proc Natl Acad Sci U S A (2005) 1.09
Identification of the minimal protein-folding nucleus through loop-entropy perturbations. Proc Natl Acad Sci U S A (2006) 1.09
Understanding protein evolution: from protein physics to Darwinian selection. Annu Rev Phys Chem (2008) 1.09
Protein biophysics explains why highly abundant proteins evolve slowly. Cell Rep (2012) 1.07
Solution of the quasispecies model for an arbitrary gene network. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 1.04
Lessons from the design of a novel atomic potential for protein folding. Protein Sci (2005) 1.02
Thymic selection of T-cell receptors as an extreme value problem. Phys Rev Lett (2009) 1.00
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. J Mol Biol (2002) 0.99
Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A (2003) 0.99
Physical origins of protein superfamilies. J Mol Biol (2006) 0.98
Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. J Am Chem Soc (2004) 0.97
Side-chain dynamics and protein folding. Proteins (2003) 0.96
Simulation, experiment, and evolution: understanding nucleation in protein S6 folding. Proc Natl Acad Sci U S A (2004) 0.95
Proteomic traces of speciation. J Mol Biol (2004) 0.95
Determining functional specificity from protein sequences. Bioinformatics (2005) 0.95
Thermal adaptation of viruses and bacteria. Biophys J (2010) 0.94
Genetic instability and the quasispecies model. J Theor Biol (2006) 0.94
Semiconservative replication in the quasispecies model. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.94
A knowledge-based move set for protein folding. Proteins (2007) 0.94
Optimality of mutation and selection in germinal centers. PLoS Comput Biol (2010) 0.93
Non-native interactions play an effective role in protein folding dynamics. Protein Sci (2010) 0.93
SDR: a database of predicted specificity-determining residues in proteins. Nucleic Acids Res (2008) 0.92
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. BMC Bioinformatics (2006) 0.92
Emergence of species in evolutionary "simulated annealing". Proc Natl Acad Sci U S A (2009) 0.92
A structure-centric view of protein evolution, design, and adaptation. Adv Enzymol Relat Areas Mol Biol (2007) 0.92
Protein evolution within a structural space. Biophys J (2003) 0.92
All-atom Monte Carlo simulation of GCAA RNA folding. J Mol Biol (2004) 0.91
The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential. Proteins (2011) 0.90
Native atom types for knowledge-based potentials: application to binding energy prediction. J Med Chem (2004) 0.89
Positively selected sites in cetacean myoglobins contribute to protein stability. PLoS Comput Biol (2013) 0.89
Combinatorial computational method gives new picomolar ligands for a known enzyme. Proc Natl Acad Sci U S A (2002) 0.89
Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response. PLoS Comput Biol (2010) 0.88
From knowledge-based potentials to combinatorial lead design in silico. Acc Chem Res (2002) 0.88
Highly abundant proteins favor more stable 3D structures in yeast. Biophys J (2013) 0.88
Common motifs and topological effects in the protein folding transition state. J Mol Biol (2006) 0.87
Equilibrium distribution of mutators in the single fitness peak model. Phys Rev Lett (2003) 0.87
Importance of DNA repair in tumor suppression. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.86
Genetic variants within the interleukin-1 gene cluster, and risk of incident myocardial infarction, and ischemic stroke: a nested case-control approach. Atherosclerosis (2008) 0.85
Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps. J Mol Biol (2009) 0.85
Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations. PLoS Comput Biol (2013) 0.84
Identifying importance of amino acids for protein folding from crystal structures. Methods Enzymol (2003) 0.84
Reversible stretching of random heteropolymers. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.84
Error and repair catastrophes: A two-dimensional phase diagram in the quasispecies model. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.83
Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions. Mol Biol Evol (2013) 0.83
Is there an en route folding intermediate for Cold shock proteins? Protein Sci (2012) 0.82
Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins. Proteins (2008) 0.82
Clinical and radiologic predictive factors of septic hip arthritis. AJR Am J Roentgenol (2012) 0.81
Compression-refractory breast hematoma secondary to pseudoaneurysm after stereotactically guided vacuum-assisted biopsy: the critical role of urgent surgical evacuation. J Clin Ultrasound (2014) 0.81
Host-parasite coevolution and optimal mutation rates for semiconservative quasispecies. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.81
Structural and energetic determinants of co-translational folding. J Chem Phys (2013) 0.80
Geometric and physical considerations for realistic protein models. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.80
Collapse of unfolded proteins in a mixture of denaturants. J Am Chem Soc (2012) 0.80
Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation. PLoS Comput Biol (2012) 0.80
Imperfect DNA lesion repair in the semiconservative quasispecies model: derivation of the Hamming class equations and solution of the single-fitness peak landscape. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.80
Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations. Proc Natl Acad Sci U S A (2007) 0.80
A universal trend among proteomes indicates an oily last common ancestor. PLoS Comput Biol (2012) 0.79
The emergence of scaling in sequence-based physical models of protein evolution. Biophys J (2005) 0.79
CoC: a database of universally conserved residues in protein folds. Bioinformatics (2005) 0.79
Phase diagram for unzipping DNA with long-range interactions. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.79
Folding and binding: the conformational repertoire of proteins: folding, aggregation and structural recognition. Curr Opin Struct Biol (2006) 0.79
The evolution dynamics of model proteins. J Chem Phys (2004) 0.79
De novo design: balancing novelty and confined chemical space. Expert Opin Drug Discov (2010) 0.78
FOG: Fragment Optimized Growth algorithm for the de novo generation of molecules occupying druglike chemical space. J Chem Inf Model (2009) 0.78
Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions. Proteins (2007) 0.78