PubRank

Eugene I Shakhnovich

Author PubWeight™ 116.12‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci U S A 2002 2.92
2 Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci U S A 2007 2.16
3 Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol 2006 2.15
4 Topological determinants of protein folding. Proc Natl Acad Sci U S A 2002 2.12
5 The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc Natl Acad Sci U S A 2002 1.86
6 Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol 2003 1.80
7 A simple physical model for scaling in protein-protein interaction networks. Proc Natl Acad Sci U S A 2005 1.78
8 Physics and evolution of thermophilic adaptation. Proc Natl Acad Sci U S A 2005 1.72
9 Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proc Natl Acad Sci U S A 2003 1.67
10 Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J Mol Biol 2002 1.66
11 The folding mechanics of a knotted protein. J Mol Biol 2007 1.64
12 A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proc Natl Acad Sci U S A 2011 1.56
13 Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J 2002 1.55
14 Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput Biol 2007 1.51
15 Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Mol Syst Biol 2008 1.50
16 Structural determinant of protein designability. Phys Rev Lett 2003 1.41
17 All-atom ab initio folding of a diverse set of proteins. Structure 2007 1.36
18 Robust protein protein interactions in crowded cellular environments. Proc Natl Acad Sci U S A 2007 1.32
19 Predicting specificity-determining residues in two large eukaryotic transcription factor families. Nucleic Acids Res 2005 1.30
20 A structure-based method for derivation of all-atom potentials for protein folding. Proc Natl Acad Sci U S A 2002 1.28
21 Energetics of protein-DNA interactions. Nucleic Acids Res 2007 1.26
22 A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds. PLoS Comput Biol 2007 1.26
23 Imprint of evolution on protein structures. Proc Natl Acad Sci U S A 2004 1.24
24 Universality and diversity of folding mechanics for three-helix bundle proteins. Proc Natl Acad Sci U S A 2008 1.24
25 Natural selection of more designable folds: a mechanism for thermophilic adaptation. Proc Natl Acad Sci U S A 2003 1.24
26 Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci U S A 2006 1.19
27 Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. J Mol Biol 2005 1.18
28 Commitment and nucleation in the protein G transition state. J Mol Biol 2004 1.18
29 Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations. Proc Natl Acad Sci U S A 2012 1.18
30 Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness. Mol Cell 2012 1.16
31 SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. J Med Chem 2002 1.14
32 Lethal mutagenesis in viruses and bacteria. Genetics 2009 1.11
33 Entropic stabilization of proteins and its proteomic consequences. PLoS Comput Biol 2005 1.11
34 All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples. J Am Chem Soc 2009 1.10
35 Nucleation and the transition state of the SH3 domain. J Mol Biol 2005 1.10
36 High-resolution protein folding with a transferable potential. Proc Natl Acad Sci U S A 2005 1.09
37 Identification of the minimal protein-folding nucleus through loop-entropy perturbations. Proc Natl Acad Sci U S A 2006 1.09
38 Understanding protein evolution: from protein physics to Darwinian selection. Annu Rev Phys Chem 2008 1.09
39 Protein biophysics explains why highly abundant proteins evolve slowly. Cell Rep 2012 1.07
40 Solution of the quasispecies model for an arbitrary gene network. Phys Rev E Stat Nonlin Soft Matter Phys 2004 1.04
41 Prokaryotic phylogenies inferred from protein structural domains. Genome Res 2005 1.02
42 Lessons from the design of a novel atomic potential for protein folding. Protein Sci 2005 1.02
43 Thymic selection of T-cell receptors as an extreme value problem. Phys Rev Lett 2009 1.00
44 Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A 2003 0.99
45 Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. J Mol Biol 2002 0.99
46 Physical origins of protein superfamilies. J Mol Biol 2006 0.98
47 Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. J Am Chem Soc 2004 0.97
48 Side-chain dynamics and protein folding. Proteins 2003 0.96
49 Determining functional specificity from protein sequences. Bioinformatics 2005 0.95
50 Proteomic traces of speciation. J Mol Biol 2004 0.95
51 Simulation, experiment, and evolution: understanding nucleation in protein S6 folding. Proc Natl Acad Sci U S A 2004 0.95
52 A knowledge-based move set for protein folding. Proteins 2007 0.94
53 Genetic instability and the quasispecies model. J Theor Biol 2006 0.94
54 Thermal adaptation of viruses and bacteria. Biophys J 2010 0.94
55 Semiconservative replication in the quasispecies model. Phys Rev E Stat Nonlin Soft Matter Phys 2004 0.94
56 Optimality of mutation and selection in germinal centers. PLoS Comput Biol 2010 0.93
57 Non-native interactions play an effective role in protein folding dynamics. Protein Sci 2010 0.93
58 SDR: a database of predicted specificity-determining residues in proteins. Nucleic Acids Res 2008 0.92
59 PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. BMC Bioinformatics 2006 0.92
60 Protein evolution within a structural space. Biophys J 2003 0.92
61 Emergence of species in evolutionary "simulated annealing". Proc Natl Acad Sci U S A 2009 0.92
62 A structure-centric view of protein evolution, design, and adaptation. Adv Enzymol Relat Areas Mol Biol 2007 0.92
63 All-atom Monte Carlo simulation of GCAA RNA folding. J Mol Biol 2004 0.91
64 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
65 Native atom types for knowledge-based potentials: application to binding energy prediction. J Med Chem 2004 0.89
66 Positively selected sites in cetacean myoglobins contribute to protein stability. PLoS Comput Biol 2013 0.89
67 Combinatorial computational method gives new picomolar ligands for a known enzyme. Proc Natl Acad Sci U S A 2002 0.89
68 From knowledge-based potentials to combinatorial lead design in silico. Acc Chem Res 2002 0.88
69 Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response. PLoS Comput Biol 2010 0.88
70 Highly abundant proteins favor more stable 3D structures in yeast. Biophys J 2013 0.88
71 Common motifs and topological effects in the protein folding transition state. J Mol Biol 2006 0.87
72 Equilibrium distribution of mutators in the single fitness peak model. Phys Rev Lett 2003 0.87
73 Importance of DNA repair in tumor suppression. Phys Rev E Stat Nonlin Soft Matter Phys 2004 0.86
74 Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps. J Mol Biol 2009 0.85
75 Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations. PLoS Comput Biol 2013 0.84
76 Identifying importance of amino acids for protein folding from crystal structures. Methods Enzymol 2003 0.84
77 Reversible stretching of random heteropolymers. Phys Rev E Stat Nonlin Soft Matter Phys 2002 0.84
78 Error and repair catastrophes: A two-dimensional phase diagram in the quasispecies model. Phys Rev E Stat Nonlin Soft Matter Phys 2004 0.83
79 Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions. Mol Biol Evol 2013 0.83
80 Is there an en route folding intermediate for Cold shock proteins? Protein Sci 2012 0.82
81 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
82 Host-parasite coevolution and optimal mutation rates for semiconservative quasispecies. Phys Rev E Stat Nonlin Soft Matter Phys 2004 0.81
83 Structural and energetic determinants of co-translational folding. J Chem Phys 2013 0.80
84 Collapse of unfolded proteins in a mixture of denaturants. J Am Chem Soc 2012 0.80
85 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
86 Geometric and physical considerations for realistic protein models. Phys Rev E Stat Nonlin Soft Matter Phys 2005 0.80
87 Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation. PLoS Comput Biol 2012 0.80
88 Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations. Proc Natl Acad Sci U S A 2007 0.80
89 The evolution dynamics of model proteins. J Chem Phys 2004 0.79
90 A universal trend among proteomes indicates an oily last common ancestor. PLoS Comput Biol 2012 0.79
91 Phase diagram for unzipping DNA with long-range interactions. Phys Rev E Stat Nonlin Soft Matter Phys 2002 0.79
92 Folding and binding: the conformational repertoire of proteins: folding, aggregation and structural recognition. Curr Opin Struct Biol 2006 0.79
93 The emergence of scaling in sequence-based physical models of protein evolution. Biophys J 2005 0.79
94 CoC: a database of universally conserved residues in protein folds. Bioinformatics 2005 0.79
95 De novo design: balancing novelty and confined chemical space. Expert Opin Drug Discov 2010 0.78
96 Semiconservative quasispecies equations for polysomic genomes: the haploid case. J Theor Biol 2006 0.78
97 Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions. Proteins 2007 0.78
98 Multi-scale sequence correlations increase proteome structural disorder and promiscuity. J Mol Biol 2011 0.78
99 FOG: Fragment Optimized Growth algorithm for the de novo generation of molecules occupying druglike chemical space. J Chem Inf Model 2009 0.78
100 Sequence correlations shape protein promiscuity. J Chem Phys 2011 0.78
101 Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms. Phys Rev E Stat Nonlin Soft Matter Phys 2005 0.77
102 Assessing the effect of loop mutations in the folding space of β2-microglobulin with molecular dynamics simulations. Int J Mol Sci 2013 0.77
103 Fold recognition with minimal gaps. Proteins 2003 0.77
104 Improvisation in evolution of genes and genomes: whose structure is it anyway? Curr Opin Struct Biol 2008 0.77
105 A one-shot germinal center model under protein structural stability constraints. Phys Biol 2013 0.77
106 Divergent evolution of a structural proteome: phenomenological models. Biophys J 2006 0.76
107 Glassy dynamics of side-chain ordering in a simple model of protein folding. Phys Rev Lett 2002 0.76
108 Repurposing of rutin for the inhibition of norovirus replication. Arch Virol 2015 0.76
109 Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations. J Mol Biol 2011 0.76
110 Slowly replicating lytic viruses: pseudolysogenic persistence and within-host competition. Phys Rev Lett 2009 0.75
111 DNA unzipping phase diagram calculated via replica theory. Phys Rev E Stat Nonlin Soft Matter Phys 2009 0.75
112 Solvation versus freezing in a heteropolymer globule. Phys Rev E Stat Nonlin Soft Matter Phys 2004 0.75
113 Selective advantage for conservative viruses. Phys Rev E Stat Nonlin Soft Matter Phys 2005 0.75
114 Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighbourhoods in Sequence Space. J Phys Chem Lett 2017 0.75
115 Sensitivity-dependent model of protein-protein interaction networks. Phys Biol 2008 0.75