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Eugene Shakhnovich

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Physiology

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Proteins

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Publications

TOP 3
Sana Raoof; Muyoung Heo; Eugene I Shakhnovich
A one-shot germinal center model under protein structural stability constraints.
Pouria Dasmeh; Kasper P Kepp; Adrian W R Serohijos; Eugene I Shakhnovich
Positively selected sites in cetacean myoglobins contribute to protein stability.
Adrian W R Serohijos; S Y Ryan Lee; Eugene I Shakhnovich
Highly abundant proteins favor more stable 3D structures in yeast.

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All Publications

2013: Sana Raoof; Muyoung Heo; Eugene I Shakhnovich
A one-shot germinal center model under protein structural stability constraints.
Physical biology 2013;10(2):025001.
2013: Pouria Dasmeh; Kasper P Kepp; Adrian W R Serohijos; Eugene I Shakhnovich
Positively selected sites in cetacean myoglobins contribute to protein stability.
PLoS computational biology 2013;9(3):e1002929.
2013: Adrian W R Serohijos; S Y Ryan Lee; Eugene I Shakhnovich
Highly abundant proteins favor more stable 3D structures in yeast.
Biophysical journal 2013;104(3):L1-3.
2013: Shimon Bershtein; Wanmeng Mu; Adrian W R Serohijos; Jingwen Zhou; Eugene I Shakhnovich
Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness.
Molecular cell 2013;49(1):133-44.
2012: Zhen Xia; Payel Das; Eugene I Shakhnovich; Ruhong Zhou
Collapse of unfolded proteins in a mixture of denaturants.
Journal of the American Chemical Society 2012;134(44):18266-74.
2012: H Krobath; S G Estácio; P F N Faísca; Eugene I Shakhnovich
Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants.
Journal of molecular biology 2012;422(5):705-22.
2012: Adrian W R Serohijos; Zilvinas Rimas; Eugene I Shakhnovich
Protein biophysics explains why highly abundant proteins evolve slowly.
Cell reports 2012;2(2):249-56.
2012: S G Estácio; Patrícia F N Faísca; C S Fernandes; H Krobath; Eugene I Shakhnovich
Robustness of atomistic Gō models in predicting native-like folding intermediates.
The Journal of chemical physics 2012;137(8):085102.
2012: Lei Huang; Eugene I Shakhnovich
Is there an en route folding intermediate for Cold shock proteins?
Protein science : a publication of the Protein Society 2012;21(5):677-85.
2012: Shimon Bershtein; Wanmeng Wu; Wanmeng Mu; Eugene I Shakhnovich
Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(13):4857-62.
2012: Ranjan V Mannige; Charles L Brooks; Eugene I Shakhnovich
A universal trend among proteomes indicates an oily last common ancestor.
PLoS computational biology 2012;8(12):e1002839.
2012: C Scott Wylie; Eugene I Shakhnovich
Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation.
PLoS computational biology 2012;8(8):e1002609.
2011: Lucas G Nivón; Eugene I Shakhnovich
Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations.
Journal of molecular biology 2011;411(5):1128-44.
2011: David B Lukatsky; Ariel Afek; Eugene I Shakhnovich
Sequence correlations shape protein promiscuity.
The Journal of chemical physics 2011;135(6):065104.
2011: C Scott Wylie; Eugene I Shakhnovich
A biophysical protein folding model accounts for most mutational fitness effects in viruses.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(24):9916-21.
2011: Arnon Afek; Eugene I Shakhnovich; David B Lukatsky
Multi-scale sequence correlations increase proteome structural disorder and promiscuity.
Journal of molecular biology 2011;409(3):439-49.
2011: Jiabin Xu; Lei Huang; Eugene I Shakhnovich
The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential.
Proteins 2011;79(6):1704-14.
2011: Muyoung Heo; Sergei Maslov; Eugene I Shakhnovich
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(10):4258-63.
2010: Patrícia F N Faísca; Ana Nunes; Rui Travasso; Eugene I Shakhnovich
Non-native interactions play an effective role in protein folding dynamics.
Protein science : a publication of the Protein Society 2010;19(11):2196-209.
2010: Peter S Kutchukian; Eugene I Shakhnovich
De novo design: balancing novelty and confined chemical space.
Expert opinion on drug discovery 2010;5(8):789-812.
2010: Jingshan Zhang; Eugene I Shakhnovich
Optimality of mutation and selection in germinal centers.
PLoS computational biology 2010;6(6):e1000800.
2010: Peiqiu Chen; Eugene I Shakhnovich
Thermal adaptation of viruses and bacteria.
Biophysical journal 2010;98(7):1109-18.
2010: Muyoung Heo; Eugene I Shakhnovich
Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response.
PLoS computational biology 2010;6(3):e1000710.
2010: Paul J Choi; X Sunney Xie; Eugene I Shakhnovich
Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps.
Journal of molecular biology 2010;396(1):230-44.
2009: Peiqiu Chen; Eugene I Shakhnovich
Lethal mutagenesis in viruses and bacteria.
Genetics 2009;183(2):639-50.
2009: Andrej Kosmrlj; Arup K Chakraborty; Mehran Kardar; Eugene I Shakhnovich
Thymic selection of T-cell receptors as an extreme value problem.
Physical review letters 2009;103(6):068103.
2009: Peter S Kutchukian; David Lou; Eugene I Shakhnovich
FOG: Fragment Optimized Growth algorithm for the de novo generation of molecules occupying druglike chemical space.
Journal of chemical information and modeling 2009;49(7):1630-42.
2009: Jingshan Zhang; Eugene I Shakhnovich
Slowly replicating lytic viruses: pseudolysogenic persistence and within-host competition.
Physical review letters 2009;102(17):178103.
2009: C Brian Roland; Kristi Adamson Hatch; Mara Prentiss; Eugene I Shakhnovich
DNA unzipping phase diagram calculated via replica theory.
Physical review. E, Statistical, nonlinear, and soft matter physics 2009;79(5 Pt 1):051923.
2009: Peter S Kutchukian; Jae Shick Yang; Gregory L Verdine; Eugene I Shakhnovich
All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples.
Journal of the American Chemical Society 2009;131(13):4622-7.
2009: Muyoung Heo; Louis Kang; Eugene I Shakhnovich
Emergence of species in evolutionary "simulated annealing".
Proceedings of the National Academy of Sciences of the United States of America 2009;106(6):1869-74.
2008: Borya Shakhnovich; Eugene I Shakhnovich
Improvisation in evolution of genes and genomes: whose structure is it anyway?
Current opinion in structural biology 2008;18(3):375-81.
2008: Antônio F Pereira de Araújo; Antonio L C Gomes; Alexandre A Bursztyn; Eugene I Shakhnovich
Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins.
Proteins 2008;70(3):971-83.
2008: D B Lukatsky; Eugene I Shakhnovich
Statistically enhanced promiscuity of structurally correlated patterns.
Physical review. E, Statistical, nonlinear, and soft matter physics 2008;77(2 Pt 1):020901.
2008: Jae Shick Yang; Stefan Wallin; Eugene I Shakhnovich
Universality and diversity of folding mechanics for three-helix bundle proteins.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(3):895-900.
2008: Jingshan Zhang; Eugene I Shakhnovich
Sensitivity-dependent model of protein-protein interaction networks.
Physical biology 2008;5(3):036011.
2008: Jingshan Zhang; Sergei Maslov; Eugene I Shakhnovich
Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size.
Molecular systems biology 2008;4():210.
2008: Konstantin B Zeldovich; Eugene I Shakhnovich
Understanding protein evolution: from protein physics to Darwinian selection.
Annual review of physical chemistry 2008;59():105-27.
2007: A R Lam; Jose M Borreguero; Feng Ding; Nikolay V Dokholyan; Sergey V Buldyrev; H Eugene Stanley; Eugene I Shakhnovich
Parallel folding pathways in the SH3 domain protein.
Journal of molecular biology 2007;373(5):1348-60.
2007: Konstantin B Zeldovich; Peiqiu Chen; Eugene I Shakhnovich
Protein stability imposes limits on organism complexity and speed of molecular evolution.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(41):16152-7.
2007: Eric J Deeds; Orr Ashenberg; Jaline Gerardin; Eugene I Shakhnovich
Robust protein protein interactions in crowded cellular environments.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(38):14952-7.
2007: Konstantin B Zeldovich; Peiqiu Chen; Borya Shakhnovich; Eugene I Shakhnovich
A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.
PLoS computational biology 2007;3(7):e139.
2007: Ethan O Perlstein; Eric J Deeds; Orr Ashenberg; Eugene I Shakhnovich; Stuart L Schreiber
Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(25):10553-8.
2007: Stefan Wallin; Konstantin B Zeldovich; Eugene I Shakhnovich
The folding mechanics of a knotted protein.
Journal of molecular biology 2007;368(3):884-93.
2007: Igor N Berezovsky; Konstantin B Zeldovich; Eugene I Shakhnovich
Positive and negative design in stability and thermal adaptation of natural proteins.
PLoS computational biology 2007;3(3):e52.
2007: Ariel Kleiner; Eugene I Shakhnovich
The mechanical unfolding of ubiquitin through all-atom Monte Carlo simulation with a Go-type potential.
Biophysical journal 2007;92(6):2054-61.
2007: William W Chen; Jae Shick Yang; Eugene I Shakhnovich
A knowledge-based move set for protein folding.
Proteins 2007;66(3):682-8.
2007: D B Lukatsky; Borya Shakhnovich; J Mintseris; Eugene I Shakhnovich
Structural similarity enhances interaction propensity of proteins.
Journal of molecular biology 2007;365(5):1596-606.
2007: Antonio L C Gomes; Júlia R de Rezende; Antônio F Pereira de Araújo; Eugene I Shakhnovich
Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions.
Proteins 2007;66(2):304-20.
2007: C Brian Roland; Eugene I Shakhnovich
Divergent evolution of a structural proteome: phenomenological models.
Biophysical journal 2007;92(3):701-16.
2007: Konstantin B Zeldovich; Igor N Berezovsky; Eugene I Shakhnovich
Protein and DNA sequence determinants of thermophilic adaptation.
PLoS computational biology 2007;3(1):e5.
2007: Jason Donald; William W Chen; Eugene I Shakhnovich
Energetics of protein-DNA interactions.
Nucleic acids research 2007;35(4):1039-47.
2007: Jae Shick Yang; William W Chen; Jeffrey Skolnick; Eugene I Shakhnovich
All-atom ab initio folding of a diverse set of proteins.
Structure (London, England : 1993) 2007;15(1):53-63.
2007: Eric J Deeds; Eugene I Shakhnovich
A structure-centric view of protein evolution, design, and adaptation.
Advances in enzymology and related areas of molecular biology 2007;75():133-91, xi-xii.
2006: Isaac A Hubner; Eric J Deeds; Eugene I Shakhnovich
Understanding ensemble protein folding at atomic detail.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(47):17747-52.
2006: D B Lukatsky; Konstantin B Zeldovich; Eugene I Shakhnovich
Statistically enhanced self-attraction of random patterns.
Physical review letters 2006;97(17):178101.
2006: Emmanuel Tannenbaum; James L Sherley; Eugene I Shakhnovich
Semiconservative quasispecies equations for polysomic genomes: the haploid case.
Journal of theoretical biology 2006;241(4):791-805.
2006: Yisroel Brumer; Franziska Michor; Eugene I Shakhnovich
Genetic instability and the quasispecies model.
Journal of theoretical biology 2006;241(2):216-22.
2006: Isaac A Hubner; Magnus Lindberg; Ellinor Haglund; Mikael Oliveberg; Eugene I Shakhnovich
Common motifs and topological effects in the protein folding transition state.
Journal of molecular biology 2006;359(4):1075-85.
2006: Eugene I Shakhnovich
Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.
Chemical reviews 2006;106(5):1559-88.
2006: Konstantin B Zeldovich; Igor N Berezovsky; Eugene I Shakhnovich
Physical origins of protein superfamilies.
Journal of molecular biology 2006;357(4):1335-43.
2006: Magnus Lindberg; Ellinor Haglund; Isaac A Hubner; Eugene I Shakhnovich; Mikael Oliveberg
Identification of the minimal protein-folding nucleus through loop-entropy perturbations.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(11):4083-8.
2006: Mikael Oliveberg; Eugene I Shakhnovich
Folding and binding: the conformational repertoire of proteins: folding, aggregation and structural recognition.
Current opinion in structural biology 2006;16(1):68-70.
2006: Eric J Deeds; Orr Ashenberg; Eugene I Shakhnovich
A simple physical model for scaling in protein-protein interaction networks.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(2):311-6.
2006: Marcin von Grotthuss; Dariusz Plewczynski; Krzysztof Ginalski; Leszek Rychlewski; Eugene I Shakhnovich
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
BMC bioinformatics 2006;7():53.
2005: Isaac A Hubner; Eric J Deeds; Eugene I Shakhnovich
High-resolution protein folding with a transferable potential.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(52):18914-9.
2005: Igor N Berezovsky; Eugene I Shakhnovich
Physics and evolution of thermophilic adaptation.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(36):12742-7.
2005: Igor N Berezovsky; William W Chen; Paul J Choi; Eugene I Shakhnovich
Entropic stabilization of proteins and its proteomic consequences.
PLoS computational biology 2005;1(4):e47.
2005: Isaac A Hubner; Eugene I Shakhnovich
Geometric and physical considerations for realistic protein models.
Physical review. E, Statistical, nonlinear, and soft matter physics 2005;72(2 Pt 1):022901.
2005: Feng Ding; Weihua Guo; Nikolay V Dokholyan; Eugene I Shakhnovich; Joan-Emma Shea
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations.
Journal of molecular biology 2005;350(5):1035-50.
2005: William W Chen; Eugene I Shakhnovich
Lessons from the design of a novel atomic potential for protein folding.
Protein science : a publication of the Protein Society 2005;14(7):1741-52.
2005: Isaac A Hubner; Katherine A Edmonds; Eugene I Shakhnovich
Nucleation and the transition state of the SH3 domain.
Journal of molecular biology 2005;349(2):424-34.
2005: Eric J Deeds; Eugene I Shakhnovich
The emergence of scaling in sequence-based physical models of protein evolution.
Biophysical journal 2005;88(6):3905-11.
2005: Jason Donald; Eugene I Shakhnovich
Determining functional specificity from protein sequences.
Bioinformatics (Oxford, England) 2005;21(11):2629-35.
2005: Jason Donald; Isaac A Hubner; Veronica M Rotemberg; Eugene I Shakhnovich; Leonid A Mirny
CoC: a database of universally conserved residues in protein folds.
Bioinformatics (Oxford, England) 2005;21(10):2539-40.
2005: Emmanuel Tannenbaum; James L Sherley; Eugene I Shakhnovich
Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms.
Physical review. E, Statistical, nonlinear, and soft matter physics 2005;71(4 Pt 1):041914.
2005: Yisroel Brumer; Eugene I Shakhnovich
Selective advantage for conservative viruses.
Physical review. E, Statistical, nonlinear, and soft matter physics 2005;71(3 Pt 1):031903.
2005: Eric J Deeds; Hooman Hennessey; Eugene I Shakhnovich
Prokaryotic phylogenies inferred from protein structural domains.
Genome research 2005;15(3):393-402.
2005: Borya Shakhnovich; Eric Deeds; Charles DeLisi; Eugene I Shakhnovich
Protein structure and evolutionary history determine sequence space topology.
Genome research 2005;15(3):385-92.
2005: Jason Donald; Eugene I Shakhnovich
Predicting specificity-determining residues in two large eukaryotic transcription factor families.
Nucleic acids research 2005;33(14):4455-65.
2004: Emmanuel Tannenbaum; James L Sherley; Eugene I Shakhnovich
Imperfect DNA lesion repair in the semiconservative quasispecies model: derivation of the Hamming class equations and solution of the single-fitness peak landscape.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;70(6 Pt 1):061915.
2004: Yisroel Brumer; Eugene I Shakhnovich
Importance of DNA repair in tumor suppression.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;70(6 Pt 1):061912.
2004: Lucas G Nivón; Eugene I Shakhnovich
All-atom Monte Carlo simulation of GCAA RNA folding.
Journal of molecular biology 2004;344(1):29-45.
2004: Brian Dominy; Eugene I Shakhnovich
Native atom types for knowledge-based potentials: application to binding energy prediction.
Journal of medicinal chemistry 2004;47(18):4538-58.
2004: Emmanuel Tannenbaum; Eugene I Shakhnovich
Solution of the quasispecies model for an arbitrary gene network.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;70(2 Pt 1):021903.
2004: Phillip L Geissler; Eugene I Shakhnovich; Alexander Yu Grosberg
Solvation versus freezing in a heteropolymer globule.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;70(2 Pt 1):021802.
2004: Guido Tiana; Nikolay V Dokholyan; Ricardo A Broglia; Eugene I Shakhnovich
The evolution dynamics of model proteins.
The Journal of chemical physics 2004;121(5):2381-9.
2004: Zhijie Liu; Brian Dominy; Eugene I Shakhnovich
Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential.
Journal of the American Chemical Society 2004;126(27):8515-28.
2004: Emmanuel Tannenbaum; Eric J Deeds; Eugene I Shakhnovich
Semiconservative replication in the quasispecies model.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;69(6 Pt 1):061916.
2004: Yisroel Brumer; Eugene I Shakhnovich
Host-parasite coevolution and optimal mutation rates for semiconservative quasispecies.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;69(6 Pt 1):061909.
2004: Isaac A Hubner; Mikael Oliveberg; Eugene I Shakhnovich
Simulation, experiment, and evolution: understanding nucleation in protein S6 folding.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(22):8354-9.
2004: Guido Tiana; Borya Shakhnovich; Nikolay V Dokholyan; Eugene I Shakhnovich
Imprint of evolution on protein structures.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(9):2846-51.
2004: Isaac A Hubner; Jun Shimada; Eugene I Shakhnovich
Commitment and nucleation in the protein G transition state.
Journal of molecular biology 2004;336(3):745-61.
2004: Eric J Deeds; Boris Shakhnovich; Eugene I Shakhnovich
Proteomic traces of speciation.
Journal of molecular biology 2004;336(3):695-706.
2004: Emmanuel Tannenbaum; Eugene I Shakhnovich
Error and repair catastrophes: A two-dimensional phase diagram in the quasispecies model.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;69(1 Pt 1):011902.
2003: Eric J Deeds; Nikolay V Dokholyan; Eugene I Shakhnovich
Protein evolution within a structural space.
Biophysical journal 2003;85(5):2962-72.
2003: Jimin Pei; Nikolay V Dokholyan; Eugene I Shakhnovich; Nick V Grishin
Using protein design for homology detection and active site searches.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11361-6.
2003: Emmanuel Tannenbaum; Eric J Deeds; Eugene I Shakhnovich
Equilibrium distribution of mutators in the single fitness peak model.
Physical review letters 2003;91(13):138105.
2003: Borya Shakhnovich; John M Harvey; Stephen R Comeau; David Lorenz; Charles DeLisi; Eugene I Shakhnovich
ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations.
BMC bioinformatics 2003;4():34.
2003: Edo Kussell; Jun Shimada; Eugene I Shakhnovich
Side-chain dynamics and protein folding.
Proteins 2003;52(2):303-21.
2003: Jeremy England; Borya Shakhnovich; Eugene I Shakhnovich
Natural selection of more designable folds: a mechanism for thermophilic adaptation.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(15):8727-31.
2003: William Chen; Leonid Mirny; Eugene I Shakhnovich
Fold recognition with minimal gaps.
Proteins 2003;51(4):531-43.
2003: Jeremy England; Eugene I Shakhnovich
Structural determinant of protein designability.
Physical review letters 2003;90(21):218101.
2003: Lewyn Li; Eugene I Shakhnovich; Leonid A Mirny
Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(8):4463-8.
2003: Borya Shakhnovich; Nikolay V Dokholyan; Charles DeLisi; Eugene I Shakhnovich
Functional fingerprints of folds: evidence for correlated structure-function evolution.
Journal of molecular biology 2003;326(1):1-9.
2003: Nikolay V Dokholyan; Jose M Borreguero; Sergey V Buldyrev; Feng Ding; H Eugene Stanley; Eugene I Shakhnovich
Identifying importance of amino acids for protein folding from crystal structures.
Methods in enzymology 2003;374():616-38.
2002: Feng Ding; Nikolay V Dokholyan; Sergey V Buldyrev; H Eugene Stanley; Eugene I Shakhnovich
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism.
Journal of molecular biology 2002;324(4):851-7.
2002: Feng Ding; Nikolay V Dokholyan; Sergey V Buldyrev; H Eugene Stanley; Eugene I Shakhnovich
Direct molecular dynamics observation of protein folding transition state ensemble.
Biophysical journal 2002;83(6):3525-32.
2002: Nikolay V Dokholyan; Borya Shakhnovich; Eugene I Shakhnovich
Expanding protein universe and its origin from the biological Big Bang.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(22):14132-6.
2002: Edo Kussell; Eugene I Shakhnovich
Glassy dynamics of side-chain ordering in a simple model of protein folding.
Physical review letters 2002;89(16):168101.
2002: Eran A Mukamel; Eugene I Shakhnovich
Phase diagram for unzipping DNA with long-range interactions.
Physical review. E, Statistical, nonlinear, and soft matter physics 2002;66(3 Pt 1):032901.
2002: Jun Shimada; Eugene I Shakhnovich
The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(17):11175-80.
2002: Nikolay V Dokholyan; Lewyn Li; Feng Ding; Eugene I Shakhnovich
Topological determinants of protein folding.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(13):8637-41.
2002: Alexey V Ishchenko; Eugene I Shakhnovich
SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions.
Journal of medicinal chemistry 2002;45(13):2770-80.
2002: Jose M Borreguero; Nikolay V Dokholyan; Sergey V Buldyrev; Eugene I Shakhnovich; H Eugene Stanley
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics.
Journal of molecular biology 2002;318(3):863-76.
2002: Phillip L Geissler; Eugene I Shakhnovich
Reversible stretching of random heteropolymers.
Physical review. E, Statistical, nonlinear, and soft matter physics 2002;65(5 Pt 2):056110.
2002: Bartosz A Grzybowski; Alexey V Ishchenko; Jun Shimada; Eugene I Shakhnovich
From knowledge-based potentials to combinatorial lead design in silico.
Accounts of chemical research 2002;35(5):261-9.
2002: Edo Kussell; Jun Shimada; Eugene I Shakhnovich
A structure-based method for derivation of all-atom potentials for protein folding.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(8):5343-8.
2002: Bartosz A Grzybowski; Alexey V Ishchenko; Chu-Young Kim; George Topalov; Robert Chapman; David W Christianson; George M Whitesides; Eugene I Shakhnovich
Combinatorial computational method gives new picomolar ligands for a known enzyme.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(3):1270-3.
2001: Lewyn Li; Eugene I Shakhnovich
Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(23):13014-8.
2001: Nikolay V Dokholyan; Eugene I Shakhnovich
Understanding hierarchical protein evolution from first principles.
Journal of molecular biology 2001;312(1):289-307.
2001: Edo Kussell; Jun Shimada; Eugene I Shakhnovich
Excluded volume in protein side-chain packing.
Journal of molecular biology 2001;311(1):183-93.
2001: G F Berriz; Eugene I Shakhnovich
Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model.
Journal of molecular biology 2001;310(3):673-85.
2001: Guido Tiana; Ricardo A Broglia; Eugene I Shakhnovich
Energy profile of the space of model protein sequences.
Journal of biological physics 2001;27(2-3):147-59.
2001: Leonid A Mirny; Eugene I Shakhnovich
Evolutionary conservation of the folding nucleus.
Journal of molecular biology 2001;308(2):123-9.
2001: Jun Shimada; Edo Kussell; Eugene I Shakhnovich
The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation.
Journal of molecular biology 2001;308(1):79-95.
2001: E Pitard; Eugene I Shakhnovich
Mode-coupling theory for heteropolymers.
Physical review. E, Statistical, nonlinear, and soft matter physics 2001;63(4 Pt 1):041501.
2001: Lewyn Li; Eugene I Shakhnovich
Different circular permutations produced different folding nuclei in proteins: a computational study.
Journal of molecular biology 2001;306(1):121-32.
2001: Leonid A Mirny; Eugene I Shakhnovich
Protein folding theory: from lattice to all-atom models.
Annual review of biophysics and biomolecular structure 2001;30():361-96.
2000: S E Choe; L Li; P T Matsudaira; Gerhard Wagner; Eugene I Shakhnovich
Differential stabilization of two hydrophobic cores in the transition state of the villin 14T folding reaction.
Journal of molecular biology 2000;304(1):99-115.
2000: J Wilder; Eugene I Shakhnovich
Proteins with selected sequences: a heteropolymeric study.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 2000;62(5 Pt B):7100-10.
2000: Leonid A Mirny; A V Finkelstein; Eugene I Shakhnovich
Statistical significance of protein structure prediction by threading.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(18):9978-83.
2000: VI Abkevich; Eugene I Shakhnovich
What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis.
Journal of molecular biology 2000;300(4):975-85.
2000: Guido Tiana; Ricardo A Broglia; Eugene I Shakhnovich
Hiking in the energy landscape in sequence space: a bumpy road to good folders.
Proteins 2000;39(3):244-51.
2000: J Shimada; Alexey V Ishchenko; Eugene I Shakhnovich
Analysis of knowledge-based protein-ligand potentials using a self-consistent method.
Protein science : a publication of the Protein Society 2000;9(4):765-75.
2000: L Li; Leonid A Mirny; Eugene I Shakhnovich
Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus.
Nature structural biology 2000;7(4):336-42.
2000: Bartosz A Grzybowski; J R Anderson; IJ Colton; S T Brittain; Eugene I Shakhnovich; George M Whitesides
Modeling the kinetics of acylation of insulin using a recursive method for solving the systems of coupled differential equations.
Biophysical journal 2000;78(2):652-61.
1999: Leonid A Mirny; Eugene I Shakhnovich
Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function.
Journal of molecular biology 1999;291(1):177-96.
1999: Aaron R Dinner; VI Abkevich; Eugene I Shakhnovich; Martin Karplus
Factors that affect the folding ability of proteins.
Proteins 1999;35(1):34-40.
1998: Leonid A Mirny; Eugene I Shakhnovich
Protein structure prediction by threading. Why it works and why it does not.
Journal of molecular biology 1998;283(2):507-26.
1998: VI Abkevich; AM Gutin; Eugene I Shakhnovich
Theory of kinetic partitioning in protein folding with possible applications to prions.
Proteins 1998;31(4):335-44.
1998: L A Mirny; V I Abkevich; Eugene I Shakhnovich
How evolution makes proteins fold quickly.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(9):4976-81.
1998: Eugene I Shakhnovich
Folding nucleus: specific or multiple? Insights from lattice models and experiments.
Folding & design 1998;3(6):R108-11; discussion R107.
1998: Nikolay V Dokholyan; S V Buldyrev; H Eugene Stanley; Eugene I Shakhnovich
Discrete molecular dynamics studies of the folding of a protein-like model.
Folding & design 1998;3(6):577-87.
1998: Stephen W Michnick; Eugene I Shakhnovich
A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies.
Folding & design 1998;3(4):239-51.
1998: Eugene I Shakhnovich
Protein design: a perspective from simple tractable models.
Folding & design 1998;3(3):R45-58.
1998: AM Gutin; VI Abkevich; Eugene I Shakhnovich
A protein engineering analysis of the transition state for protein folding: simulation in the lattice model.
Folding & design 1998;3(3):183-94.
1997: Eugene I Shakhnovich
Theoretical studies of protein-folding thermodynamics and kinetics.
Current opinion in structural biology 1997;7(1):29-40.
1996: Leonid A Mirny; Eugene I Shakhnovich
How to derive a protein folding potential? A new approach to an old problem.
Journal of molecular biology 1996;264(5):1164-79.
1996: VI Abkevich; A M Gutin; Eugene I Shakhnovich
How the first biopolymers could have evolved.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(2):839-44.
1996: C D Sfatos; A M Gutin; VI Abkevich; Eugene I Shakhnovich
Simulations of chaperone-assisted folding.
Biochemistry 1996;35(1):334-9.
1996: Eugene I Shakhnovich; VI Abkevich; O Ptitsyn
Conserved residues and the mechanism of protein folding.
Nature 1996;379(6560):96-8.
1996: VI Abkevich; A M Gutin; Eugene I Shakhnovich
Improved design of stable and fast-folding model proteins.
Folding & design 1996;1(3):221-30.
1996: Eugene I Shakhnovich
Modeling protein folding: the beauty and power of simplicity.
Folding & design 1996;1(3):R50-4.
1996: Leonid A Mirny; VI Abkevich; Eugene I Shakhnovich
Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model.
Folding & design 1996;1(2):103-16.
1995: VI Abkevich; A M Gutin; Eugene I Shakhnovich
Impact of local and non-local interactions on thermodynamics and kinetics of protein folding.
Journal of molecular biology 1995;252(4):460-71.
1995: R S DeWitte; S W Michnick; Eugene I Shakhnovich
Exhaustive enumeration of protein conformations using experimental restraints.
Protein science : a publication of the Protein Society 1995;4(9):1780-91.
1995: VI Abkevich; A M Gutin; Eugene I Shakhnovich
Domains in folding of model proteins.
Protein science : a publication of the Protein Society 1995;4(6):1167-77.
1995: A M Gutin; VI Abkevich; Eugene I Shakhnovich
Is burst hydrophobic collapse necessary for protein folding?
Biochemistry 1995;34(9):3066-76.
1995: A M Gutin; VI Abkevich; Eugene I Shakhnovich
Evolution-like selection of fast-folding model proteins.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(5):1282-6.
1994: R S DeWitte; Eugene I Shakhnovich
Pseudodihedrals: simplified protein backbone representation with knowledge-based energy.
Protein science : a publication of the Protein Society 1994;3(9):1570-81.
1994: VI Abkevich; A M Gutin; Eugene I Shakhnovich
Specific nucleus as the transition state for protein folding: evidence from the lattice model.
Biochemistry 1994;33(33):10026-36.
1994: Andrej Sali; Eugene I Shakhnovich; M Karplus
How does a protein fold?
Nature 1994;369(6477):248-51.
1994: Andrej Sali; Eugene I Shakhnovich; M Karplus
Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.
Journal of molecular biology 1994;235(5):1614-36.
1993: Eugene I Shakhnovich; A M Gutin
A new approach to the design of stable proteins.
Protein engineering 1993;6(8):793-800.
1993: Eugene I Shakhnovich; A M Gutin
Engineering of stable and fast-folding sequences of model proteins.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(15):7195-9.
1991: Eugene I Shakhnovich; A M Gutin
Influence of point mutations on protein structure: probability of a neutral mutation.
Journal of theoretical biology 1991;149(4):537-46.
1990: Eugene I Shakhnovich; A M Gutin
Implications of thermodynamics of protein folding for evolution of primary sequences.
Nature 1990;346(6286):773-5.
1989: Eugene I Shakhnovich; A M Gutin
Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach.
Biophysical chemistry 1989;34(3):187-99.