Published in Proc Natl Acad Sci U S A on October 03, 2007
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
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Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response. PLoS Comput Biol (2010) 0.88
Population size dependence of fitness effect distribution and substitution rate probed by biophysical model of protein thermostability. Genome Biol Evol (2013) 0.88
Amino acid composition of proteins reduces deleterious impact of mutations. Sci Rep (2013) 0.86
Protein folding and binding can emerge as evolutionary spandrels through structural coupling. Proc Natl Acad Sci U S A (2015) 0.86
Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations. PLoS Comput Biol (2013) 0.84
Alanine scan of core positions in ubiquitin reveals links between dynamics, stability, and function. J Mol Biol (2013) 0.84
Does mutational robustness inhibit extinction by lethal mutagenesis in viral populations? PLoS Comput Biol (2010) 0.83
Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions. Mol Biol Evol (2013) 0.83
A zinc-binding site by negative selection induces metallodrug susceptibility in an essential chaperonin. Proc Natl Acad Sci U S A (2010) 0.82
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Stochastic simulations suggest that HIV-1 survives close to its error threshold. PLoS Comput Biol (2012) 0.81
Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses. MBio (2015) 0.81
The influence of selection for protein stability on dN/dS estimations. Genome Biol Evol (2014) 0.81
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Biophysical fitness landscapes for transcription factor binding sites. PLoS Comput Biol (2014) 0.81
Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences. PLoS Comput Biol (2015) 0.81
Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation. PLoS Comput Biol (2012) 0.80
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Computational design of a pH stable enzyme: understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions. PLoS One (2014) 0.80
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The linear interaction energy method for the prediction of protein stability changes upon mutation. Proteins (2011) 0.79
Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation. Cancer Res (2015) 0.79
A model of proteostatic energy cost and its use in analysis of proteome trends and sequence evolution. PLoS One (2014) 0.78
Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties. J Mol Evol (2015) 0.78
Highly diverse protein library based on the ubiquitous (β/α)₈ enzyme fold yields well-structured proteins through in vitro folding selection. Chembiochem (2013) 0.78
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Protein Destabilization as a Common Factor in Diverse Inherited Disorders. J Mol Evol (2015) 0.76
Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges. PLoS One (2015) 0.76
Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations. Curr Opin Struct Biol (2016) 0.76
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The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution. Biophys J (2017) 0.75
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A simple physical model for scaling in protein-protein interaction networks. Proc Natl Acad Sci U S A (2005) 1.78
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The folding mechanics of a knotted protein. J Mol Biol (2007) 1.64
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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
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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
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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
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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
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Lessons from the design of a novel atomic potential for protein folding. Protein Sci (2005) 1.02
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Simulation, experiment, and evolution: understanding nucleation in protein S6 folding. Proc Natl Acad Sci U S A (2004) 0.95
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A knowledge-based move set for protein folding. Proteins (2007) 0.94
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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
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Positively selected sites in cetacean myoglobins contribute to protein stability. PLoS Comput Biol (2013) 0.89
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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
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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
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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
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Multi-scale sequence correlations increase proteome structural disorder and promiscuity. J Mol Biol (2011) 0.78
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