Published in Phys Rev E Stat Nonlin Soft Matter Phys on August 11, 2004
Quasispecies theory in the context of population genetics. BMC Evol Biol (2005) 2.02
Quasispecies made simple. PLoS Comput Biol (2005) 1.56
A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds. PLoS Comput Biol (2007) 1.26
Error-threshold exists in fitness landscapes with lethal mutants. BMC Evol Biol (2007) 1.07
The relationship between the error catastrophe, survival of the flattest, and natural selection. BMC Evol Biol (2011) 1.04
Examining the theory of error catastrophe. J Virol (2006) 1.00
Lethal mutagenesis in a structured environment. J Theor Biol (2009) 0.82
Repression/depression of conjugative plasmids and their influence on the mutation-selection balance in static environments. PLoS One (2014) 0.77
Critical mutation rate has an exponential dependence on population size in haploid and diploid populations. PLoS One (2013) 0.75
Effect of the SOS response on the mean fitness of unicellular populations: a quasispecies approach. PLoS One (2010) 0.75
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
Prokaryotic phylogenies inferred from protein structural domains. Genome Res (2005) 1.02
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
Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A (2003) 0.99
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. J Mol Biol (2002) 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
Determining functional specificity from protein sequences. Bioinformatics (2005) 0.95
Proteomic traces of speciation. J Mol Biol (2004) 0.95
Genetic instability and the quasispecies model. J Theor Biol (2006) 0.94
A knowledge-based move set for protein folding. Proteins (2007) 0.94
Thermal adaptation of viruses and bacteria. Biophys J (2010) 0.94
Semiconservative replication in the quasispecies model. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 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
A structure-centric view of protein evolution, design, and adaptation. Adv Enzymol Relat Areas Mol Biol (2007) 0.92
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. BMC Bioinformatics (2006) 0.92
SDR: a database of predicted specificity-determining residues in proteins. Nucleic Acids Res (2008) 0.92
Emergence of species in evolutionary "simulated annealing". Proc Natl Acad Sci U S A (2009) 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
From knowledge-based potentials to combinatorial lead design in silico. Acc Chem Res (2002) 0.88
Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response. PLoS Comput Biol (2010) 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
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
Host-parasite coevolution and optimal mutation rates for semiconservative quasispecies. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.81
Geometric and physical considerations for realistic protein models. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.80
Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations. Proc Natl Acad Sci U S A (2007) 0.80
Structural and energetic determinants of co-translational folding. J Chem Phys (2013) 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
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
The evolution dynamics of model proteins. J Chem Phys (2004) 0.79
The emergence of scaling in sequence-based physical models of protein evolution. Biophys J (2005) 0.79
Folding and binding: the conformational repertoire of proteins: folding, aggregation and structural recognition. Curr Opin Struct Biol (2006) 0.79
Phase diagram for unzipping DNA with long-range interactions. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.79
A universal trend among proteomes indicates an oily last common ancestor. PLoS Comput Biol (2012) 0.79
CoC: a database of universally conserved residues in protein folds. Bioinformatics (2005) 0.79
Multi-scale sequence correlations increase proteome structural disorder and promiscuity. J Mol Biol (2011) 0.78
Sequence correlations shape protein promiscuity. J Chem Phys (2011) 0.78
De novo design: balancing novelty and confined chemical space. Expert Opin Drug Discov (2010) 0.78
Semiconservative quasispecies equations for polysomic genomes: the haploid case. J Theor Biol (2006) 0.78
Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions. Proteins (2007) 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