Eugene Shakhnovich

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Physiology

Chemicals & Drugs

Proteins

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Publications

TOP 3
Chen Peiqiu; Shakhnovich Eugene I
Lethal mutagenesis in viruses and bacteria.
Kosmrlj Andrej; Chakraborty Arup K; Kardar Mehran; Shakhnovich Eugene I
Thymic selection of T-cell receptors as an extreme value problem.
Kutchukian Peter S; Lou David; Shakhnovich Eugene I
FOG: Fragment Optimized Growth algorithm for the de novo generation of molecules occupying druglike chemical space.

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All Publications

2009: Chen Peiqiu; Shakhnovich Eugene I
Lethal mutagenesis in viruses and bacteria.
Genetics 2009;183(2):639-50.
2009: Kosmrlj Andrej; Chakraborty Arup K; Kardar Mehran; Shakhnovich Eugene I
Thymic selection of T-cell receptors as an extreme value problem.
Physical review letters 2009;103(6):068103.
2009: Kutchukian Peter S; Lou David; Shakhnovich Eugene I
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: Zhang Jingshan; Shakhnovich Eugene I
Slowly replicating lytic viruses: pseudolysogenic persistence and within-host competition.
Physical review letters 2009;102(17):178103.
2009: Roland C Brian; Hatch Kristi Adamson; Prentiss Mara; Shakhnovich Eugene I
DNA unzipping phase diagram calculated via replica theory.
Physical review. E, Statistical, nonlinear, and soft matter physics 2009;79(5 Pt 1):051923.
2009: Kutchukian Peter S; Yang Jae Shick; Verdine Gregory L; Shakhnovich Eugene I
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: Heo Muyoung; Kang Louis; Shakhnovich Eugene I
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: Shakhnovich Boris E; Shakhnovich Eugene I
Improvisation in evolution of genes and genomes: whose structure is it anyway?
Current opinion in structural biology 2008;18(3):375-81.
2008: Lukatsky D B; Shakhnovich E I
Statistically enhanced promiscuity of structurally correlated patterns.
Physical review. E, Statistical, nonlinear, and soft matter physics 2008;77(2 Pt 1):020901.
2008: Pereira de Araújo Antônio F; Gomes Antonio L C; Bursztyn Alexandre A; Shakhnovich Eugene I
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: Yang Jae Shick; Wallin Stefan; Shakhnovich Eugene I
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: Zhang Jingshan; Shakhnovich Eugene I
Sensitivity-dependent model of protein-protein interaction networks.
Physical biology 2008;5(3):36011.
2008: Zhang Jingshan; Maslov Sergei; Shakhnovich Eugene I
Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size.
Molecular systems biology 2008;4():210.
2008: Zeldovich Konstantin B; Shakhnovich Eugene I
Understanding protein evolution: from protein physics to Darwinian selection.
Annual review of physical chemistry 2008;59():105-27.
2007: Lam A R; Borreguero J M; Ding F; Dokholyan N V; Buldyrev S V; Stanley H E; Shakhnovich E
Parallel folding pathways in the SH3 domain protein.
Journal of molecular biology 2007;373(5):1348-60.
2007: Zeldovich Konstantin B; Chen Peiqiu; Shakhnovich Eugene I
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: Deeds Eric J; Ashenberg Orr; Gerardin Jaline; Shakhnovich Eugene I
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: Zeldovich Konstantin B; Chen Peiqiu; Shakhnovich Boris E; Shakhnovich Eugene I
A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.
PLoS computational biology 2007;3(7):e139.
2007: Perlstein Ethan O; Deeds Eric J; Ashenberg Orr; Shakhnovich Eugene I; Schreiber Stuart L
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: Wallin Stefan; Zeldovich Konstantin B; Shakhnovich Eugene I
The folding mechanics of a knotted protein.
Journal of molecular biology 2007;368(3):884-93.
2007: Berezovsky Igor N; Zeldovich Konstantin B; Shakhnovich Eugene I
Positive and negative design in stability and thermal adaptation of natural proteins.
PLoS computational biology 2007;3(3):e52.
2007: Kleiner Ariel; Shakhnovich Eugene
The mechanical unfolding of ubiquitin through all-atom Monte Carlo simulation with a Go-type potential.
Biophysical journal 2007;92(6):2054-61.
2007: Chen William W; Yang Jae Shick; Shakhnovich Eugene I
A knowledge-based move set for protein folding.
Proteins 2007;66(3):682-8.
2007: Lukatsky D B; Shakhnovich B E; Mintseris J; Shakhnovich E I
Structural similarity enhances interaction propensity of proteins.
Journal of molecular biology 2007;365(5):1596-606.
2007: Gomes Antonio L C; de Rezende Júlia R; Pereira de Araújo Antônio F; Shakhnovich Eugene I
Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions.
Proteins 2007;66(2):304-20.
2007: Roland C Brian; Shakhnovich Eugene I
Divergent evolution of a structural proteome: phenomenological models.
Biophysical journal 2007;92(3):701-16.
2007: Yang Jae Shick; Chen William W; Skolnick Jeffrey; Shakhnovich Eugene I
All-atom ab initio folding of a diverse set of proteins.
Structure (London, England : 1993) 2007;15(1):53-63.
2007: Zeldovich Konstantin B; Berezovsky Igor N; Shakhnovich Eugene I
Protein and DNA sequence determinants of thermophilic adaptation.
PLoS computational biology 2007;3(1):e5.
2007: Donald Jason E; Chen William W; Shakhnovich Eugene I
Energetics of protein-DNA interactions.
Nucleic acids research 2007;35(4):1039-47.
2007: Deeds Eric J; Shakhnovich Eugene I
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: Hubner Isaac A; Deeds Eric J; Shakhnovich Eugene I
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: Lukatsky D B; Zeldovich K B; Shakhnovich E I
Statistically enhanced self-attraction of random patterns.
Physical review letters 2006;97(17):178101.
2006: Tannenbaum Emmanuel; Sherley James L; Shakhnovich Eugene I
Semiconservative quasispecies equations for polysomic genomes: the haploid case.
Journal of theoretical biology 2006;241(4):791-805.
2006: Brumer Yisroel; Michor Franziska; Shakhnovich Eugene I
Genetic instability and the quasispecies model.
Journal of theoretical biology 2006;241(2):216-22.
2006: Hubner Isaac A; Lindberg Magnus; Haglund Ellinor; Oliveberg Mikael; Shakhnovich Eugene I
Common motifs and topological effects in the protein folding transition state.
Journal of molecular biology 2006;359(4):1075-85.
2006: Shakhnovich Eugene
Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.
Chemical reviews 2006;106(5):1559-88.
2006: Zeldovich Konstantin B; Berezovsky Igor N; Shakhnovich Eugene I
Physical origins of protein superfamilies.
Journal of molecular biology 2006;357(4):1335-43.
2006: Lindberg Magnus O; Haglund Ellinor; Hubner Isaac A; Shakhnovich Eugene I; Oliveberg Mikael
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: Oliveberg Mikael; Shakhnovich Eugene I
Folding and binding: the conformational repertoire of proteins: folding, aggregation and structural recognition.
Current opinion in structural biology 2006;16(1):68-70.
2006: Deeds Eric J; Ashenberg Orr; Shakhnovich Eugene I
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: von Grotthuss Marcin; Plewczynski Dariusz; Ginalski Krzysztof; Rychlewski Leszek; Shakhnovich Eugene I
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
BMC bioinformatics 2006;7():53.
2005: Hubner Isaac A; Deeds Eric J; Shakhnovich Eugene I
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: Berezovsky Igor N; Chen William W; Choi Paul J; Shakhnovich Eugene I
Entropic stabilization of proteins and its proteomic consequences.
PLoS computational biology 2005;1(4):e47.
2005: Berezovsky Igor N; Shakhnovich Eugene I
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: Hubner Isaac A; Shakhnovich Eugene I
Geometric and physical considerations for realistic protein models.
Physical review. E, Statistical, nonlinear, and soft matter physics 2005;72(2 Pt 1):022901.
2005: Chen William W; Shakhnovich Eugene I
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: Ding Feng; Guo Weihua; Dokholyan Nikolay V; Shakhnovich Eugene I; Shea Joan-Emma
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: Hubner Isaac A; Edmonds Katherine A; Shakhnovich Eugene I
Nucleation and the transition state of the SH3 domain.
Journal of molecular biology 2005;349(2):424-34.
2005: Deeds Eric J; Shakhnovich Eugene I
The emergence of scaling in sequence-based physical models of protein evolution.
Biophysical journal 2005;88(6):3905-11.
2005: Donald Jason E; Shakhnovich Eugene I
Determining functional specificity from protein sequences.
Bioinformatics (Oxford, England) 2005;21(11):2629-35.
2005: Donald Jason E; Hubner Isaac A; Rotemberg Veronica M; Shakhnovich Eugene I; Mirny Leonid A
CoC: a database of universally conserved residues in protein folds.
Bioinformatics (Oxford, England) 2005;21(10):2539-40.
2005: Tannenbaum Emmanuel; Sherley James L; Shakhnovich Eugene I
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: Brumer Yisroel; Shakhnovich Eugene I
Selective advantage for conservative viruses.
Physical review. E, Statistical, nonlinear, and soft matter physics 2005;71(3 Pt 1):031903.
2005: Deeds Eric J; Hennessey Hooman; Shakhnovich Eugene I
Prokaryotic phylogenies inferred from protein structural domains.
Genome research 2005;15(3):393-402.
2005: Shakhnovich Boris E; Deeds Eric; Delisi Charles; Shakhnovich Eugene
Protein structure and evolutionary history determine sequence space topology.
Genome research 2005;15(3):385-92.
2005: Donald Jason E; Shakhnovich Eugene I
Predicting specificity-determining residues in two large eukaryotic transcription factor families.
Nucleic acids research 2005;33(14):4455-65.
2004: Tannenbaum Emmanuel; Sherley James L; Shakhnovich Eugene I
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: Brumer Yisroel; Shakhnovich Eugene I
Importance of DNA repair in tumor suppression.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;70(6 Pt 1):061912.
2004: Nivón Lucas G; Shakhnovich Eugene I
All-atom Monte Carlo simulation of GCAA RNA folding.
Journal of molecular biology 2004;344(1):29-45.
2004: Tannenbaum Emmanuel; Shakhnovich Eugene I
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: Geissler Phillip L; Shakhnovich Eugene I; Grosberg Alexander Yu
Solvation versus freezing in a heteropolymer globule.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;70(2 Pt 1):021802.
2004: Dominy Brian N; Shakhnovich Eugene I
Native atom types for knowledge-based potentials: application to binding energy prediction.
Journal of medicinal chemistry 2004;47(18):4538-58.
2004: Tiana Guido; Dokholyan Nikolay V; Broglia Ricardo A; Shakhnovich Eugene I
The evolution dynamics of model proteins.
The Journal of chemical physics 2004;121(5):2381-9.
2004: Liu Zhijie; Dominy Brian N; Shakhnovich Eugene I
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: Tannenbaum Emmanuel; Deeds Eric J; Shakhnovich Eugene I
Semiconservative replication in the quasispecies model.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;69(6 Pt 1):061916.
2004: Brumer Yisroel; Shakhnovich Eugene I
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: Hubner Isaac A; Oliveberg Mikael; Shakhnovich Eugene I
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: Tiana Guido; Shakhnovich Boris E; Dokholyan Nikolay V; Shakhnovich Eugene I
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: Hubner Isaac A; Shimada Jun; Shakhnovich Eugene I
Commitment and nucleation in the protein G transition state.
Journal of molecular biology 2004;336(3):745-61.
2004: Deeds Eric J; Shakhnovich Boris; Shakhnovich Eugene I
Proteomic traces of speciation.
Journal of molecular biology 2004;336(3):695-706.
2004: Tannenbaum Emmanuel; Shakhnovich Eugene I
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: Deeds Eric J; Dokholyan Nikolay V; Shakhnovich Eugene I
Protein evolution within a structural space.
Biophysical journal 2003;85(5):2962-72.
2003: Tannenbaum Emmanuel; Deeds Eric J; Shakhnovich Eugene I
Equilibrium distribution of mutators in the single fitness peak model.
Physical review letters 2003;91(13):138105.
2003: Pei Jimin; Dokholyan Nikolay V; Shakhnovich Eugene I; Grishin Nick V
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: Shakhnovich Boris E; Harvey John M; Comeau Steve; Lorenz David; DeLisi Charles; Shakhnovich Eugene
ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations.
BMC bioinformatics 2003;4():34.
2003: Kussell Edo; Shimada Jun; Shakhnovich Eugene I
Side-chain dynamics and protein folding.
Proteins 2003;52(2):303-21.
2003: England Jeremy L; Shakhnovich Boris E; Shakhnovich Eugene I
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: Chen William; Mirny Leonid; Shakhnovich Eugene I
Fold recognition with minimal gaps.
Proteins 2003;51(4):531-43.
2003: England Jeremy L; Shakhnovich Eugene I
Structural determinant of protein designability.
Physical review letters 2003;90(21):218101.
2003: Li Lewyn; Shakhnovich Eugene I; Mirny Leonid A
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: Shakhnovich Boris E; Dokholyan Nikolay V; DeLisi Charles; Shakhnovich Eugene I
Functional fingerprints of folds: evidence for correlated structure-function evolution.
Journal of molecular biology 2003;326(1):1-9.
2003: Dokholyan Nikolay V; Borreguero Jose M; Buldyrev Sergey V; Ding Feng; Stanley H Eugene; Shakhnovich Eugene I
Identifying importance of amino acids for protein folding from crystal structures.
Methods in enzymology 2003;374():616-38.
2002: Ding Feng; Dokholyan Nikolay V; Buldyrev Sergey V; Stanley H Eugene; Shakhnovich Eugene I
Direct molecular dynamics observation of protein folding transition state ensemble.
Biophysical journal 2002;83(6):3525-32.
2002: Ding Feng; Dokholyan Nikolay V; Buldyrev Sergey V; Stanley H Eugene; Shakhnovich Eugene I
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism.
Journal of molecular biology 2002;324(4):851-7.
2002: Kussell Edo; Shakhnovich Eugene I
Glassy dynamics of side-chain ordering in a simple model of protein folding.
Physical review letters 2002;89(16):168101.
2002: Dokholyan Nikolay V; Shakhnovich Boris; Shakhnovich Eugene I
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: Mukamel Eran A; Shakhnovich Eugene I
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: Shimada Jun; Shakhnovich Eugene I
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: Dokholyan Nikolay V; Li Lewyn; Ding Feng; Shakhnovich Eugene I
Topological determinants of protein folding.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(13):8637-41.
2002: Ishchenko Alexey V; Shakhnovich Eugene I
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: Geissler Phillip L; Shakhnovich Eugene I
Reversible stretching of random heteropolymers.
Physical review. E, Statistical, nonlinear, and soft matter physics 2002;65(5 Pt 2):056110.
2002: Borreguero Jose M; Dokholyan Nikolay V; Buldyrev Sergey V; Shakhnovich Eugene I; Stanley H Eugene
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics.
Journal of molecular biology 2002;318(3):863-76.
2002: Grzybowski Bartosz A; Ishchenko Alexey V; Shimada Jun; Shakhnovich Eugene I
From knowledge-based potentials to combinatorial lead design in silico.
Accounts of chemical research 2002;35(5):261-9.
2002: Kussell Edo; Shimada Jun; Shakhnovich Eugene I
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: Grzybowski Bartosz A; Ishchenko Alexey V; Kim Chu-Young; Topalov George; Chapman Robert; Christianson David W; Whitesides George M; Shakhnovich Eugene I
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: Li L; Shakhnovich E I
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: Dokholyan N V; Shakhnovich E I
Understanding hierarchical protein evolution from first principles.
Journal of molecular biology 2001;312(1):289-307.
2001: Kussell E; Shimada J; Shakhnovich E I
Excluded volume in protein side-chain packing.
Journal of molecular biology 2001;311(1):183-93.
2001: Berriz G F; Shakhnovich E I
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: Mirny L; Shakhnovich E
Evolutionary conservation of the folding nucleus.
Journal of molecular biology 2001;308(2):123-9.
2001: Pitard E; Shakhnovich E I
Mode-coupling theory for heteropolymers.
Physical review. E, Statistical, nonlinear, and soft matter physics 2001;63(4 Pt 1):041501.
2001: Shimada J; Kussell E L; Shakhnovich E I
The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation.
Journal of molecular biology 2001;308(1):79-95.
2001: Li L; Shakhnovich E I
Different circular permutations produced different folding nuclei in proteins: a computational study.
Journal of molecular biology 2001;306(1):121-32.
2001: Mirny L; Shakhnovich E
Protein folding theory: from lattice to all-atom models.
Annual review of biophysics and biomolecular structure 2001;30():361-96.
2000: Wilder J; Shakhnovich E I
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: Choe S E; Li L; Matsudaira P T; Wagner G; Shakhnovich E I
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: Mirny L A; Finkelstein A V; Shakhnovich E I
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: Abkevich V I; Shakhnovich E I
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: Tiana G; Broglia R A; Shakhnovich E I
Hiking in the energy landscape in sequence space: a bumpy road to good folders.
Proteins 2000;39(3):244-51.
2000: Shimada J; Ishchenko A V; Shakhnovich E I
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: Li L; Mirny L A; Shakhnovich E I
Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus.
Nature structural biology 2000;7(4):336-42.
2000: Grzybowski B A; Anderson J R; Colton I; Brittain S T; Shakhnovich E I; Whitesides G M
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: Mirny L A; Shakhnovich E I
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: Dinner A R; Abkevich V; Shakhnovich E; Karplus M
Factors that affect the folding ability of proteins.
Proteins 1999;35(1):34-40.
1998: Mirny L A; Shakhnovich E I
Protein structure prediction by threading. Why it works and why it does not.
Journal of molecular biology 1998;283(2):507-26.
1998: Abkevich V I; Gutin A M; Shakhnovich E I
Theory of kinetic partitioning in protein folding with possible applications to prions.
Proteins 1998;31(4):335-44.
1998: Mirny L A; Abkevich V I; Shakhnovich E I
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: Shakhnovich E I
Folding nucleus: specific or multiple? Insights from lattice models and experiments.
Folding & design 1998;3(6):R108-11; discussion R107.
1998: Dokholyan N V; Buldyrev S V; Stanley H E; Shakhnovich E I
Discrete molecular dynamics studies of the folding of a protein-like model.
Folding & design 1998;3(6):577-87.
1998: Michnick S W; Shakhnovich E
A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies.
Folding & design 1998;3(4):239-51.
1998: Shakhnovich E I
Protein design: a perspective from simple tractable models.
Folding & design 1998;3(3):R45-58.
1998: Gutin A M; Abkevich V I; Shakhnovich E I
A protein engineering analysis of the transition state for protein folding: simulation in the lattice model.
Folding & design 1998;3(3):183-94.
1997: Shakhnovich E I
Theoretical studies of protein-folding thermodynamics and kinetics.
Current opinion in structural biology 1997;7(1):29-40.
1996: Mirny L A; Shakhnovich E I
How to derive a protein folding potential? A new approach to an old problem.
Journal of molecular biology 1996;264(5):1164-79.
1996: Abkevich V I; Gutin A M; Shakhnovich E I
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: Sfatos C D; Gutin A M; Abkevich V I; Shakhnovich E I
Simulations of chaperone-assisted folding.
Biochemistry 1996;35(1):334-9.
1996: Shakhnovich E; Abkevich V; Ptitsyn O
Conserved residues and the mechanism of protein folding.
Nature 1996;379(6560):96-8.
1996: Abkevich V I; Gutin A M; Shakhnovich E I
Improved design of stable and fast-folding model proteins.
Folding & design 1996;1(3):221-30.
1996: Shakhnovich E I
Modeling protein folding: the beauty and power of simplicity.
Folding & design 1996;1(3):R50-4.
1996: Mirny L A; Abkevich V; Shakhnovich E I
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: DeWitte R S; Michnick S W; Shakhnovich E I
Exhaustive enumeration of protein conformations using experimental restraints.
Protein science : a publication of the Protein Society 1995;4(9):1780-91.
1995: Abkevich V I; Gutin A M; Shakhnovich E I
Impact of local and non-local interactions on thermodynamics and kinetics of protein folding.
Journal of molecular biology 1995;252(4):460-71.
1995: Abkevich V I; Gutin A M; Shakhnovich E I
Domains in folding of model proteins.
Protein science : a publication of the Protein Society 1995;4(6):1167-77.
1995: Gutin A M; Abkevich V I; Shakhnovich E I
Is burst hydrophobic collapse necessary for protein folding?
Biochemistry 1995;34(9):3066-76.
1995: Gutin A M; Abkevich V I; Shakhnovich E I
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: DeWitte R S; Shakhnovich E I
Pseudodihedrals: simplified protein backbone representation with knowledge-based energy.
Protein science : a publication of the Protein Society 1994;3(9):1570-81.
1994: Abkevich V I; Gutin A M; Shakhnovich E I
Specific nucleus as the transition state for protein folding: evidence from the lattice model.
Biochemistry 1994;33(33):10026-36.
1994: Sali A; Shakhnovich E; Karplus M
How does a protein fold?
Nature 1994;369(6477):248-51.
1994: Sali A; Shakhnovich E; Karplus M
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: Shakhnovich E I; Gutin A M
A new approach to the design of stable proteins.
Protein engineering 1993;6(8):793-800.
1993: Shakhnovich E I; Gutin A M
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: Shakhnovich E I; Gutin A M
Influence of point mutations on protein structure: probability of a neutral mutation.
Journal of theoretical biology 1991;149(4):537-46.
1990: Shakhnovich E I; Gutin A M
Implications of thermodynamics of protein folding for evolution of primary sequences.
Nature 1990;346(6286):773-5.
1989: Shakhnovich E I; Gutin A M
Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach.
Biophysical chemistry 1989;34(3):187-99.

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