Eugene I. Shakhnovich - Publications

Affiliations: 
Harvard University, Cambridge, MA, United States 
Area:
Protein Folding and Design, Molecular Evolution, Drug Discovery
Website:
http://chemistry.harvard.edu/people/eugene-i-shakhnovich

233 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Chen Q, Xiao Y, Shakhnovich EI, Zhang W, Mu W. Semi-rational design and molecular dynamics simulations study of the thermostability enhancement of cellobiose 2-epimerases. International Journal of Biological Macromolecules. PMID 31733243 DOI: 10.1016/j.ijbiomac.2019.11.015  0.68
2019 Xiao Y, Chen Q, Shakhnovich EI, Zhang W, Mu W. Simulation-guided enzyme discovery: A new microbial source of cellobiose 2-epimerase. International Journal of Biological Macromolecules. PMID 31401280 DOI: 10.1016/j.ijbiomac.2019.08.075  0.68
2019 Adkar BV, Bhattacharyya S, Gilson AI, Zhang W, Shakhnovich EI. Substrate inhibition imposes fitness penalty at high protein stability. Proceedings of the National Academy of Sciences of the United States of America. PMID 31097595 DOI: 10.1073/pnas.1821447116  0.76
2018 Manhart M, Shakhnovich EI. Growth tradeoffs produce complex microbial communities on a single limiting resource. Nature Communications. 9: 3214. PMID 30097583 DOI: 10.1038/s41467-018-05703-6  0.4
2018 Jacobs WM, Shakhnovich EI. Accurate Protein-Folding Transition-Path Statistics From a Simple Free-Energy Landscape. The Journal of Physical Chemistry. B. PMID 30091592 DOI: 10.1021/acs.jpcb.8b05842  0.32
2018 Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI. ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. Bioinformatics (Oxford, England). PMID 30010795 DOI: 10.1093/bioinformatics/bty516  0.76
2018 Rotem A, Serohijos AWR, Chang CB, Wolfe JT, Fischer AE, Mehoke TS, Zhang H, Tao Y, Ung WL, Choi JM, Rodrigues JV, Abimbola OK, Koehler SA, Wu S, Thielen PM, ... ... Shakhnovich EI, et al. Evolution on the biophysical fitness landscape of an RNA virus. Molecular Biology and Evolution. PMID 29955873 DOI: 10.1093/molbev/msy131  0.88
2018 Bhattacharyya S, Jacobs WM, Adkar BV, Yan J, Zhang W, Shakhnovich EI. Accessibility of the Shine-Dalgarno Sequence Dictates N-Terminal Codon Bias in E. coli. Molecular Cell. 70: 894-905.e5. PMID 29883608 DOI: 10.1016/j.molcel.2018.05.008  0.6
2018 Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI. ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. Bioinformatics (Oxford, England). PMID 29741573 DOI: 10.1093/bioinformatics/bty370  0.76
2018 Manhart M, Adkar BV, Shakhnovich EI. Trade-offs between microbial growth phases lead to frequency-dependent and non-transitive selection. Proceedings. Biological Sciences. 285. PMID 29445020 DOI: 10.1098/rspb.2017.2459  0.4
2017 Jacobs WM, Shakhnovich EI. Evidence of evolutionary selection for cotranslational folding. Proceedings of the National Academy of Sciences of the United States of America. 114: 11434-11439. PMID 29073068 DOI: 10.1073/pnas.1705772114  0.32
2017 Adkar BV, Manhart M, Bhattacharyya S, Tian J, Musharbash M, Shakhnovich EI. Optimization of lag phase shapes the evolution of a bacterial enzyme. Nature Ecology & Evolution. 1: 149. PMID 28812634 DOI: 10.1038/s41559-017-0149  0.4
2017 Chéron N, Shakhnovich EI. Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations. Journal of Computational Chemistry. PMID 28568844 DOI: 10.1002/jcc.24839  0.52
2017 Gilson AI, Marshall-Christensen A, Choi JM, Shakhnovich EI. The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution. Biophysical Journal. 112: 1350-1365. PMID 28402878 DOI: 10.1016/j.bpj.2017.02.029  0.76
2017 Choi JM, Gilson AI, Shakhnovich EI. Graph's Topology and Free Energy of a Spin Model on the Graph. Physical Review Letters. 118: 088302. PMID 28282198 DOI: 10.1103/PhysRevLett.118.088302  0.76
2017 Debroise T, Shakhnovich EI, Chéron N. A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016. Journal of Chemical Information and Modeling. PMID 28191941 DOI: 10.1021/acs.jcim.6b00610  0.52
2017 Zhou Q, Sun X, Xia X, Fan Z, Luo Z, Zhao S, Shakhnovich EI, Liang H. Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighbourhoods in Sequence Space. The Journal of Physical Chemistry Letters. PMID 28045264 DOI: 10.1021/acs.jpclett.6b02769  0.6
2016 Bhattacharyya S, Bershtein S, Yan J, Argun T, Gilson AI, Trauger SA, Shakhnovich EI. Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity. Elife. 5. PMID 27938662 DOI: 10.7554/eLife.20309  0.76
2016 Bershtein S, Serohijos AW, Shakhnovich EI. Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations. Current Opinion in Structural Biology. 42: 31-40. PMID 27810574 DOI: 10.1016/j.sbi.2016.10.013  0.92
2016 Jacobs WM, Shakhnovich EI. Structure-Based Prediction of Protein-Folding Transition Paths. Biophysical Journal. 111: 925-36. PMID 27602721 DOI: 10.1016/j.bpj.2016.06.031  0.32
2016 Serebryany E, Woodard JC, Adkar BV, Shabab M, King JA, Shakhnovich EI. An internal disulfide locks a misfolded aggregation-prone intermediate in cataract-linked mutants of human γD-crystallin. The Journal of Biological Chemistry. PMID 27417136 DOI: 10.1074/jbc.M116.735977  1
2016 Chéron N, Serohijos AW, Choi JM, Shakhnovich EI. Evolutionary dynamics of viral escape under antibodies stress: A biophysical model. Protein Science : a Publication of the Protein Society. PMID 26939576 DOI: 10.1002/pro.2915  0.92
2016 Rodrigues JV, Bershtein S, Li A, Lozovsky ER, Hartl DL, Shakhnovich EI. Biophysical principles predict fitness landscapes of drug resistance. Proceedings of the National Academy of Sciences of the United States of America. PMID 26929328 DOI: 10.1073/pnas.1601441113  1
2015 Zhou Q, Xia X, Luo Z, Liang H, Shakhnovich E. Searching the Sequence Space for Potent Aptamers Using SELEX in Silico. Journal of Chemical Theory and Computation. 11: 5939-46. PMID 26642994 DOI: 10.1021/acs.jctc.5b00707  1
2015 Bershtein S, Serohijos AW, Bhattacharyya S, Manhart M, Choi JM, Mu W, Zhou J, Shakhnovich EI. Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria. Plos Genetics. 11: e1005612. PMID 26484862 DOI: 10.1371/journal.pgen.1005612  1
2015 Chéron N, Jasty N, Shakhnovich EI. OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. Journal of Medicinal Chemistry. PMID 26356253 DOI: 10.1021/acs.jmedchem.5b00886  0.52
2015 Chéron N, Yu C, Kolawole AO, Shakhnovich EI, Wobus CE. Repurposing of rutin for the inhibition of norovirus replication. Archives of Virology. PMID 26112762 DOI: 10.1007/s00705-015-2495-y  1
2015 Zhang H, Cockrell SK, Kolawole AO, Rotem A, Serohijos AW, Chang CB, Tao Y, Mehoke TS, Han Y, Lin JS, Giacobbi NS, Feldman AB, Shakhnovich E, Weitz DA, Wobus CE, et al. Isolation and Analysis of Rare Norovirus Recombinants from Coinfected Mice Using Drop-Based Microfluidics. Journal of Virology. 89: 7722-34. PMID 25972549 DOI: 10.1128/JVI.01137-15  1
2015 Tian J, Woodard JC, Whitney A, Shakhnovich EI. Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences. Plos Computational Biology. 11: e1004207. PMID 25905910 DOI: 10.1371/journal.pcbi.1004207  1
2015 Bershtein S, Choi JM, Bhattacharyya S, Budnik B, Shakhnovich E. Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship. Cell Reports. 11: 645-56. PMID 25892240 DOI: 10.1016/j.celrep.2015.03.051  1
2015 Choi JM, Serohijos AW, Murphy S, Lucarelli D, Lofranco LL, Feldman A, Shakhnovich EI. Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding. Biophysical Journal. 108: 795-8. PMID 25692584 DOI: 10.1016/j.bpj.2015.01.001  1
2015 Çetinba? M, Shakhnovich EI. Is catalytic activity of chaperones a selectable trait for the emergence of heat shock response? Biophysical Journal. 108: 438-48. PMID 25606691 DOI: 10.1016/j.bpj.2014.11.3468  1
2015 Tricard S, Shepherd RF, Stan CA, Snyder PW, Cademartiri R, Zhu D, Aranson IS, Shakhnovich EI, Whitesides GM. Mechanical model of globular transition in polymers Chempluschem. 80: 37-41. DOI: 10.1002/cplu.201402203  1
2014 Bhattacharyya S, Bershtein S, Shakhnovich EI. Gene Dosage Experiments in Enterobacteriaceae Using Arabinose-regulated Promoters. Bio-Protocol. 7. PMID 29170750 DOI: 10.21769/BioProtoc.2396  0.68
2014 Dasmeh P, Serohijos AW, Kepp KP, Shakhnovich EI. The influence of selection for protein stability on dN/dS estimations. Genome Biology and Evolution. 6: 2956-67. PMID 25355808 DOI: 10.1093/gbe/evu223  0.92
2014 Peleg O, Choi JM, Shakhnovich EI. Evolution of specificity in protein-protein interactions. Biophysical Journal. 107: 1686-96. PMID 25296322 DOI: 10.1016/j.bpj.2014.08.004  1
2014 Serohijos AW, Shakhnovich EI. Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics. Current Opinion in Structural Biology. 26: 84-91. PMID 24952216 DOI: 10.1016/j.sbi.2014.05.005  1
2014 Estácio SG, Krobath H, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PF. A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior. Plos Computational Biology. 10: e1003606. PMID 24809460 DOI: 10.1371/journal.pcbi.1003606  1
2014 Klein EY, Serohijos AW, Choi JM, Shakhnovich EI, Pekosz A. Influenza A H1N1 pandemic strain evolution--divergence and the potential for antigenic drift variants. Plos One. 9: e93632. PMID 24699432 DOI: 10.1371/journal.pone.0093632  1
2014 Serohijos AW, Shakhnovich EI. Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions. Molecular Biology and Evolution. 31: 165-76. PMID 24124208 DOI: 10.1093/molbev/mst189  1
2013 Cetinba? M, Shakhnovich EI. Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations. Plos Computational Biology. 9: e1003269. PMID 24244114 DOI: 10.1371/journal.pcbi.1003269  1
2013 Estácio SG, Shakhnovich EI, Faísca PF. Assessing the effect of loop mutations in the folding space of β2-microglobulin with molecular dynamics simulations. International Journal of Molecular Sciences. 14: 17256-78. PMID 23975166 DOI: 10.3390/ijms140917256  1
2013 Krobath H, Shakhnovich EI, Faísca PF. Structural and energetic determinants of co-translational folding. The Journal of Chemical Physics. 138: 215101. PMID 23758397 DOI: 10.1063/1.4808044  1
2013 Dasmeh P, Serohijos AW, Kepp KP, Shakhnovich EI. Positively selected sites in cetacean myoglobins contribute to protein stability. Plos Computational Biology. 9: e1002929. PMID 23505347 DOI: 10.1371/journal.pcbi.1002929  1
2013 Raoof S, Heo M, Shakhnovich EI. A one-shot germinal center model under protein structural stability constraints. Physical Biology. 10: 025001. PMID 23492682 DOI: 10.1088/1478-3975/10/2/025001  1
2013 Serohijos AW, Lee SY, Shakhnovich EI. Highly abundant proteins favor more stable 3D structures in yeast. Biophysical Journal. 104: L1-3. PMID 23442924 DOI: 10.1016/j.bpj.2012.11.3838  1
2013 Bershtein S, Mu W, Serohijos AW, Zhou J, Shakhnovich EI. Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness. Molecular Cell. 49: 133-44. PMID 23219534 DOI: 10.1016/j.molcel.2012.11.004  1
2013 Tricard S, Stan CA, Shakhnovich EI, Whitesides GM. A macroscopic device described by a Boltzmann-like distribution Soft Matter. 9: 4480-4488. DOI: 10.1039/c3sm27385g  1
2012 Mannige RV, Brooks CL, Shakhnovich EI. A universal trend among proteomes indicates an oily last common ancestor. Plos Computational Biology. 8: e1002839. PMID 23300421 DOI: 10.1371/journal.pcbi.1002839  1
2012 Xia Z, Das P, Shakhnovich EI, Zhou R. Collapse of unfolded proteins in a mixture of denaturants. Journal of the American Chemical Society. 134: 18266-74. PMID 23057830 DOI: 10.1021/ja3031505  1
2012 Serohijos AW, Rimas Z, Shakhnovich EI. Protein biophysics explains why highly abundant proteins evolve slowly. Cell Reports. 2: 249-56. PMID 22938865 DOI: 10.1016/j.celrep.2012.06.022  1
2012 Estácio SG, Fernandes CS, Krobath H, Faísca PF, Shakhnovich EI. Robustness of atomistic Gō models in predicting native-like folding intermediates. The Journal of Chemical Physics. 137: 085102. PMID 22938266 DOI: 10.1063/1.4747492  1
2012 Wylie CS, Shakhnovich EI. Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation. Plos Computational Biology. 8: e1002609. PMID 22876168 DOI: 10.1371/journal.pcbi.1002609  1
2012 Krobath H, Estácio SG, Faísca PF, Shakhnovich EI. Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants. Journal of Molecular Biology. 422: 705-22. PMID 22727745 DOI: 10.1016/j.jmb.2012.06.020  1
2012 Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, ... ... Shakhnovich E, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/pro.2071  1
2012 Huang L, Shakhnovich EI. Is there an en route folding intermediate for Cold shock proteins? Protein Science : a Publication of the Protein Society. 21: 677-85. PMID 22467601 DOI: 10.1002/pro.2053  1
2012 Bershtein S, Mu W, Wu W, Shakhnovich EI. Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations. Proceedings of the National Academy of Sciences of the United States of America. 109: 4857-62. PMID 22411825 DOI: 10.1073/pnas.1118157109  1
2012 Bershtein S, Wu W, Shakhnovich EI. 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, (4857-4862) DOI: 10.1073/pnas. 1118157109) Proceedings of the National Academy of Sciences of the United States of America. 109: 7126. DOI: 10.1073/pnas.1205753109  1
2011 Lukatsky DB, Afek A, Shakhnovich EI. Sequence correlations shape protein promiscuity. The Journal of Chemical Physics. 135: 065104. PMID 21842953 DOI: 10.1063/1.3624332  1
2011 Nivón LG, Shakhnovich EI. Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations. Journal of Molecular Biology. 411: 1128-44. PMID 21740912 DOI: 10.1016/j.jmb.2011.06.042  1
2011 Wylie CS, Shakhnovich EI. 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. 108: 9916-21. PMID 21610162 DOI: 10.1073/pnas.1017572108  1
2011 Afek A, Shakhnovich EI, Lukatsky DB. Multi-scale sequence correlations increase proteome structural disorder and promiscuity. Journal of Molecular Biology. 409: 439-49. PMID 21463640 DOI: 10.1016/j.jmb.2011.03.056  1
2011 Heo M, Maslov S, Shakhnovich E. 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. 108: 4258-4263. PMID 21368118 DOI: 10.1073/pnas.1009392108  1
2011 Xu J, Huang L, Shakhnovich EI. The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential. Proteins. 79: 1704-14. PMID 21365688 DOI: 10.1002/prot.22993  1
2011 Shakhnovich E. Protein folding: To knot or not to knot? Nature Materials. 10: 84-86. DOI: 10.1038/nmat2953  1
2011 Kutchukian PS, Lou D, Shakhnovich EI. In silico fragment-based generation of drug-like compounds Acs Symposium Series. 1076: 151-177. DOI: 10.1021/bk-2011-1076.ch008  1
2011 Heo M, Zeldovich KB, Shakhnovich EI. Diversity Against Adversity: How Adaptive Immune System Evolves Potent Antibodies Journal of Statistical Physics. 144: 241-267. DOI: 10.1007/s10955-011-0241-8  1
2010 Kutchukian PS, Shakhnovich EI. De novo design: balancing novelty and confined chemical space. Expert Opinion On Drug Discovery. 5: 789-812. PMID 22827800 DOI: 10.1517/17460441.2010.497534  1
2010 Faísca PF, Nunes A, Travasso RD, Shakhnovich EI. Non-native interactions play an effective role in protein folding dynamics. Protein Science : a Publication of the Protein Society. 19: 2196-209. PMID 20836137 DOI: 10.1002/pro.498  1
2010 Zhang J, Shakhnovich EI. Optimality of mutation and selection in germinal centers. Plos Computational Biology. 6: e1000800. PMID 20532164 DOI: 10.1371/journal.pcbi.1000800  1
2010 Chen P, Shakhnovich EI. Thermal adaptation of viruses and bacteria. Biophysical Journal. 98: 1109-18. PMID 20371310 DOI: 10.1016/j.bpj.2009.11.048  1
2010 Heo M, Shakhnovich EI. Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response. Plos Computational Biology. 6: e1000710. PMID 20300650 DOI: 10.1371/journal.pcbi.1000710  1
2010 Choi PJ, Xie XS, Shakhnovich EI. Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps. Journal of Molecular Biology. 396: 230-44. PMID 19931280 DOI: 10.1016/j.jmb.2009.11.035  1
2009 Kosmrlj A, Chakraborty AK, Kardar M, Shakhnovich EI. Thymic selection of T-cell receptors as an extreme value problem. Physical Review Letters. 103: 068103. PMID 19792616 DOI: 10.1103/PhysRevLett.103.068103  1
2009 Chen P, Shakhnovich EI. Lethal mutagenesis in viruses and bacteria. Genetics. 183: 639-50. PMID 19620390 DOI: 10.1534/genetics.109.106492  1
2009 Shakhnovich E. Protein folding roller coaster, one molecule at a time Proceedings of the National Academy of Sciences of the United States of America. 106: 11823-11824. PMID 19617547 DOI: 10.1073/pnas.0906228106  1
2009 Kutchukian PS, Lou D, Shakhnovich EI. FOG: Fragment Optimized Growth algorithm for the de novo generation of molecules occupying druglike chemical space. Journal of Chemical Information and Modeling. 49: 1630-42. PMID 19527020 DOI: 10.1021/ci9000458  1
2009 Zhang J, Shakhnovich EI. Slowly replicating lytic viruses: pseudolysogenic persistence and within-host competition. Physical Review Letters. 102: 178103. PMID 19518838 DOI: 10.1103/PhysRevLett.102.178103  1
2009 Roland CB, Hatch KA, Prentiss M, Shakhnovich EI. DNA unzipping phase diagram calculated via replica theory. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 79: 051923. PMID 19518496 DOI: 10.1103/PhysRevE.79.051923  1
2009 Kutchukian PS, Yang JS, Verdine GL, Shakhnovich EI. All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples. Journal of the American Chemical Society. 131: 4622-7. PMID 19334772 DOI: 10.1021/ja805037p  1
2009 Lee JW, Zemojtel T, Shakhnovich E. Systems-level evidence of transcriptional co-regulation of yeast protein complexes Journal of Computational Biology. 16: 331-339. PMID 19193150 DOI: 10.1089/cmb.2008.17TT  1
2009 Heo M, Kang L, Shakhnovich EI. Emergence of species in evolutionary "simulated annealing". Proceedings of the National Academy of Sciences of the United States of America. 106: 1869-74. PMID 19164759 DOI: 10.1073/pnas.0809852106  1
2009 Donald JE, Shakhnovich EI. SDR: a database of predicted specificity-determining residues in proteins. Nucleic Acids Research. 37: D191-4. PMID 18927118 DOI: 10.1093/nar/gkn716  1
2008 Faísca PF, Travasso RD, Ball RC, Shakhnovich EI. Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis. The Journal of Chemical Physics. 129: 095108. PMID 19044896 DOI: 10.1063/1.2973624  1
2008 Zhang J, Shakhnovich EI. Sensitivity-dependent model of protein-protein interaction networks. Physical Biology. 5: 036011. PMID 18824789 DOI: 10.1088/1478-3975/5/3/036011  1
2008 Zhang J, Maslov S, Shakhnovich EI. Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Molecular Systems Biology. 4: 210. PMID 18682700 DOI: 10.1038/msb.2008.48  1
2008 Shakhnovich BE, Shakhnovich EI. Improvisation in evolution of genes and genomes: whose structure is it anyway? Current Opinion in Structural Biology. 18: 375-81. PMID 18487041 DOI: 10.1016/j.sbi.2008.02.007  1
2008 Lukatsky DB, Shakhnovich EI. Statistically enhanced promiscuity of structurally correlated patterns. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 020901. PMID 18351980 DOI: 10.1103/PhysRevE.77.020901  1
2008 Yang JS, Wallin S, Shakhnovich EI. Universality and diversity of folding mechanics for three-helix bundle proteins. Proceedings of the National Academy of Sciences of the United States of America. 105: 895-900. PMID 18195374 DOI: 10.1073/pnas.0707284105  1
2008 Zeldovich KB, Shakhnovich EI. Understanding protein evolution: from protein physics to Darwinian selection. Annual Review of Physical Chemistry. 59: 105-27. PMID 17937598 DOI: 10.1146/annurev.physchem.58.032806.104449  1
2008 Pereira de Araújo AF, Gomes AL, Bursztyn AA, Shakhnovich EI. Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins. Proteins. 70: 971-83. PMID 17847091 DOI: 10.1002/prot.21571  1
2007 Zeldovich KB, Chen P, Shakhnovich EI. 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. 104: 16152-7. PMID 17913881 DOI: 10.1073/pnas.0705366104  1
2007 Lam AR, Borreguero JM, Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich E. Parallel folding pathways in the SH3 domain protein. Journal of Molecular Biology. 373: 1348-60. PMID 17900612 DOI: 10.1016/j.jmb.2007.08.032  1
2007 Deeds EJ, Ashenberg O, Gerardin J, Shakhnovich EI. Robust protein protein interactions in crowded cellular environments. Proceedings of the National Academy of Sciences of the United States of America. 104: 14952-7. PMID 17848524 DOI: 10.1073/pnas.0702766104  1
2007 Zeldovich KB, Chen P, Shakhnovich BE, Shakhnovich EI. A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds. Plos Computational Biology. 3: e139. PMID 17630830 DOI: 10.1371/journal.pcbi.0030139  1
2007 Perlstein EO, Deeds EJ, Ashenberg O, Shakhnovich EI, Schreiber SL. Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations. Proceedings of the National Academy of Sciences of the United States of America. 104: 10553-8. PMID 17566105 DOI: 10.1073/pnas.0704037104  1
2007 Berezovsky IN, Zeldovich KB, Shakhnovich EI. Positive and negative design in stability and thermal adaptation of natural proteins. Plos Computational Biology. 3: e52. PMID 17381236 DOI: 10.1371/journal.pcbi.0030052  1
2007 Wallin S, Zeldovich KB, Shakhnovich EI. The folding mechanics of a knotted protein. Journal of Molecular Biology. 368: 884-93. PMID 17368671 DOI: 10.1016/j.jmb.2007.02.035  1
2007 Kleiner A, Shakhnovich E. The mechanical unfolding of ubiquitin through all-atom Monte Carlo simulation with a Go-type potential. Biophysical Journal. 92: 2054-61. PMID 17293405 DOI: 10.1529/biophysj.106.081257  1
2007 Donald JE, Chen WW, Shakhnovich EI. Energetics of protein-DNA interactions. Nucleic Acids Research. 35: 1039-47. PMID 17259221 DOI: 10.1093/nar/gkl1103  1
2007 Yang JS, Chen WW, Skolnick J, Shakhnovich EI. All-atom ab initio folding of a diverse set of proteins. Structure (London, England : 1993). 15: 53-63. PMID 17223532 DOI: 10.1016/j.str.2006.11.010  1
2007 Zeldovich KB, Berezovsky IN, Shakhnovich EI. Protein and DNA sequence determinants of thermophilic adaptation. Plos Computational Biology. 3: e5. PMID 17222055 DOI: 10.1371/journal.pcbi.0030005  1
2007 Chen WW, Yang JS, Shakhnovich EI. A knowledge-based move set for protein folding. Proteins. 66: 682-8. PMID 17143895 DOI: 10.1002/prot.21237  1
2007 Lukatsky DB, Shakhnovich BE, Mintseris J, Shakhnovich EI. Structural similarity enhances interaction propensity of proteins. Journal of Molecular Biology. 365: 1596-606. PMID 17141268 DOI: 10.1016/j.jmb.2006.11.020  1
2007 Deeds EJ, Shakhnovich EI. A structure-centric view of protein evolution, design, and adaptation. Advances in Enzymology and Related Areas of Molecular Biology. 75: 133-91, xi-xii. PMID 17124867  1
2007 Gomes AL, de Rezende JR, Pereira de Araújo AF, Shakhnovich EI. Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions. Proteins. 66: 304-20. PMID 17109406 DOI: 10.1002/prot.21137  1
2007 Roland CB, Shakhnovich EI. Divergent evolution of a structural proteome: phenomenological models. Biophysical Journal. 92: 701-16. PMID 17071665 DOI: 10.1529/biophysj.106.081265  1
2007 Zeldovich KB, Berezovsky IN, Shakhnovich EI. How organisms adapt to the environment: Sequence determinants of the habitat temperature and its physical rationale Proceedings of the International School of Physics "Enrico Fermi". 165: 47-83.  1
2006 Lukatsky DB, Zeldovich KB, Shakhnovich EI. Statistically enhanced self-attraction of random patterns. Physical Review Letters. 97: 178101. PMID 17155509 DOI: 10.1103/PhysRevLett.97.178101  1
2006 Hubner IA, Deeds EJ, Shakhnovich EI. Understanding ensemble protein folding at atomic detail. Proceedings of the National Academy of Sciences of the United States of America. 103: 17747-52. PMID 17095606 DOI: 10.1073/pnas.0605580103  1
2006 Shakhnovich E. Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet Chemical Reviews. 106: 1559-1588. PMID 16683745 DOI: 10.1021/cr040425u  1
2006 Hubner IA, Lindberg M, Haglund E, Oliveberg M, Shakhnovich EI. Common motifs and topological effects in the protein folding transition state. Journal of Molecular Biology. 359: 1075-85. PMID 16678203 DOI: 10.1016/j.jmb.2006.04.015  1
2006 Tannenbaum E, Sherley JL, Shakhnovich EI. Semiconservative quasispecies equations for polysomic genomes: the haploid case. Journal of Theoretical Biology. 241: 791-805. PMID 16527313 DOI: 10.1016/j.jtbi.2006.01.016  1
2006 Lindberg MO, Haglund E, Hubner IA, Shakhnovich EI, Oliveberg M. Identification of the minimal protein-folding nucleus through loop-entropy perturbations. Proceedings of the National Academy of Sciences of the United States of America. 103: 4083-8. PMID 16505376 DOI: 10.1073/pnas.0508863103  1
2006 Zeldovich KB, Berezovsky IN, Shakhnovich EI. Physical origins of protein superfamilies. Journal of Molecular Biology. 357: 1335-43. PMID 16483605 DOI: 10.1016/j.jmb.2006.01.081  1
2006 Zhang Y, Hubner IA, Arakaki AK, Shakhnovich E, Skolnick J. On the origin and highly likely completeness of single-domain protein structures. Proceedings of the National Academy of Sciences of the United States of America. 103: 2605-10. PMID 16478803 DOI: 10.1073/pnas.0509379103  1
2006 von Grotthuss M, Plewczynski D, Ginalski K, Rychlewski L, Shakhnovich EI. PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. Bmc Bioinformatics. 7: 53. PMID 16460560 DOI: 10.1186/1471-2105-7-53  1
2006 Oliveberg M, Shakhnovich EI. Folding and binding: the conformational repertoire of proteins: folding, aggregation and structural recognition. Current Opinion in Structural Biology. 16: 68-70. PMID 16443362 DOI: 10.1016/j.sbi.2006.01.015  1
2006 Brumer Y, Michor F, Shakhnovich EI. Genetic instability and the quasispecies model. Journal of Theoretical Biology. 241: 216-22. PMID 16386760 DOI: 10.1016/j.jtbi.2005.11.018  1
2006 Deeds EJ, Ashenberg O, Shakhnovich EI. A simple physical model for scaling in protein-protein interaction networks. Proceedings of the National Academy of Sciences of the United States of America. 103: 311-6. PMID 16384916 DOI: 10.1073/pnas.0509715102  1
2006 Shakhnovich E. Monte-Carlo methods in studies of protein folding and evolution Lecture Notes in Physics. 704: 563-593. DOI: 10.1007/3-540-35284-8_21  1
2005 Hubner IA, Deeds EJ, Shakhnovich EI. High-resolution protein folding with a transferable potential. Proceedings of the National Academy of Sciences of the United States of America. 102: 18914-9. PMID 16365306 DOI: 10.1073/pnas.0502181102  1
2005 Berezovsky IN, Chen WW, Choi PJ, Shakhnovich EI. Entropic stabilization of proteins and its proteomic consequences. Plos Computational Biology. 1: e47. PMID 16201009 DOI: 10.1371/journal.pcbi.0010047  1
2005 Hubner IA, Shakhnovich EI. Geometric and physical considerations for realistic protein models. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 022901. PMID 16196617 DOI: 10.1103/PhysRevE.72.022901  1
2005 Berezovsky IN, Shakhnovich EI. Physics and evolution of thermophilic adaptation. Proceedings of the National Academy of Sciences of the United States of America. 102: 12742-7. PMID 16120678 DOI: 10.1073/pnas.0503890102  1
2005 Donald JE, Shakhnovich EI. Predicting specificity-determining residues in two large eukaryotic transcription factor families. Nucleic Acids Research. 33: 4455-65. PMID 16085755 DOI: 10.1093/nar/gki755  1
2005 Chen WW, Shakhnovich EI. Lessons from the design of a novel atomic potential for protein folding. Protein Science : a Publication of the Protein Society. 14: 1741-52. PMID 15987903 DOI: 10.1110/ps.051440705  1
2005 Ding F, Guo W, Dokholyan NV, Shakhnovich EI, Shea JE. Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. Journal of Molecular Biology. 350: 1035-50. PMID 15982666 DOI: 10.1016/j.jmb.2005.05.017  1
2005 Tannenbaum E, Sherley JL, Shakhnovich EI. Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 71: 041914. PMID 15903708 DOI: 10.1103/PhysRevE.71.041914  1
2005 Brumer Y, Shakhnovich EI. Selective advantage for conservative viruses. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 71: 031903. PMID 15903455 DOI: 10.1103/PhysRevE.71.031903  1
2005 Hubner IA, Edmonds KA, Shakhnovich EI. Nucleation and the transition state of the SH3 domain. Journal of Molecular Biology. 349: 424-34. PMID 15890206 DOI: 10.1016/j.jmb.2005.03.050  1
2005 Deeds EJ, Shakhnovich EI. The emergence of scaling in sequence-based physical models of protein evolution. Biophysical Journal. 88: 3905-11. PMID 15805176 DOI: 10.1529/biophysj.104.051433  1
2005 Donald JE, Shakhnovich EI. Determining functional specificity from protein sequences. Bioinformatics (Oxford, England). 21: 2629-35. PMID 15797914 DOI: 10.1093/bioinformatics/bti396  1
2005 Donald JE, Hubner IA, Rotemberg VM, Shakhnovich EI, Mirny LA. CoC: a database of universally conserved residues in protein folds. Bioinformatics (Oxford, England). 21: 2539-40. PMID 15746286 DOI: 10.1093/bioinformatics/bti360  1
2005 Deeds EJ, Hennessey H, Shakhnovich EI. Prokaryotic phylogenies inferred from protein structural domains. Genome Research. 15: 393-402. PMID 15741510 DOI: 10.1101/gr.3033805  1
2005 Tannenbaum E, Shakhnovich EI. Semiconservative replication, genetic repair, and many-gened genomes: Extending the quasispecies paradigm to living systems Physics of Life Reviews. 2: 290-317. DOI: 10.1016/j.plrev.2005.08.001  1
2004 Tannenbaum E, Sherley JL, Shakhnovich EI. 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. 70: 061915. PMID 15697410 DOI: 10.1103/PhysRevE.70.061915  1
2004 Brumer Y, Shakhnovich EI. Importance of DNA repair in tumor suppression. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 061912. PMID 15697407 DOI: 10.1103/PhysRevE.70.061912  1
2004 Nivón LG, Shakhnovich EI. All-atom Monte Carlo simulation of GCAA RNA folding. Journal of Molecular Biology. 344: 29-45. PMID 15504400 DOI: 10.1016/j.jmb.2004.09.041  1
2004 Tannenbaum E, Shakhnovich EI. Solution of the quasispecies model for an arbitrary gene network. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 021903. PMID 15447511 DOI: 10.1103/PhysRevE.70.021903  1
2004 Geissler PL, Shakhnovich EI, Grosberg AY. Solvation versus freezing in a heteropolymer globule. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 021802. PMID 15447508 DOI: 10.1103/PhysRevE.70.021802  1
2004 Dominy BN, Shakhnovich EI. Native atom types for knowledge-based potentials: application to binding energy prediction. Journal of Medicinal Chemistry. 47: 4538-58. PMID 15317465 DOI: 10.1021/jm0498046  1
2004 Tiana G, Dokholyan NV, Broglia RA, Shakhnovich EI. The evolution dynamics of model proteins. The Journal of Chemical Physics. 121: 2381-9. PMID 15260793 DOI: 10.1063/1.1768513  1
2004 Tannenbaum E, Deeds EJ, Shakhnovich EI. Semiconservative replication in the quasispecies model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 061916. PMID 15244626 DOI: 10.1103/PhysRevE.69.061916  1
2004 Brumer Y, Shakhnovich EI. Host-parasite coevolution and optimal mutation rates for semiconservative quasispecies. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 061909. PMID 15244619 DOI: 10.1103/PhysRevE.69.061909  1
2004 Liu Z, Dominy BN, Shakhnovich EI. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. Journal of the American Chemical Society. 126: 8515-28. PMID 15238009 DOI: 10.1021/ja032018q  1
2004 Hubner IA, Oliveberg M, Shakhnovich EI. Simulation, experiment, and evolution: understanding nucleation in protein S6 folding. Proceedings of the National Academy of Sciences of the United States of America. 101: 8354-9. PMID 15150413 DOI: 10.1073/pnas.0401672101  1
2004 Hubner IA, Shimada J, Shakhnovich EI. Commitment and nucleation in the protein G transition state. Journal of Molecular Biology. 336: 745-61. PMID 15095985 DOI: 10.1016/j.jmb.2003.12.032  1
2004 Deeds EJ, Shakhnovich B, Shakhnovich EI. Proteomic traces of speciation. Journal of Molecular Biology. 336: 695-706. PMID 15095981 DOI: 10.1016/j.jmb.2003.12.066  1
2004 Tannenbaum E, Shakhnovich EI. Error and repair catastrophes: A two-dimensional phase diagram in the quasispecies model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 011902. PMID 14995642  1
2004 Tiana G, Shakhnovich BE, Dokholyan NV, Shakhnovich EI. Imprint of evolution on protein structures. Proceedings of the National Academy of Sciences of the United States of America. 101: 2846-51. PMID 14970345 DOI: 10.1073/pnas.0306638101  1
2004 Morrissey MP, Ahmed Z, Shakhnovich EI. The role of cotranslation in protein folding: A lattice model study Polymer. 45: 557-571. DOI: 10.1016/j.polymer.2003.10.090  1
2003 Dokholyan NV, Borreguero JM, Buldyrev SV, Ding F, Stanley HE, Shakhnovich EI. Identifying importance of amino acids for protein folding from crystal structures. Methods in Enzymology. 374: 616-38. PMID 14696390 DOI: 10.1016/S0076-6879(03)74025-7  1
2003 Deeds EJ, Dokholyan NV, Shakhnovich EI. Protein evolution within a structural space. Biophysical Journal. 85: 2962-72. PMID 14581198 DOI: 10.1016/S0006-3495(03)74716-X  1
2003 Tannenbaum E, Deeds EJ, Shakhnovich EI. Equilibrium distribution of mutators in the single fitness peak model. Physical Review Letters. 91: 138105. PMID 14525341 DOI: 10.1103/PhysRevLett.91.138105  1
2003 Pei J, Dokholyan NV, Shakhnovich EI, Grishin NV. Using protein design for homology detection and active site searches. Proceedings of the National Academy of Sciences of the United States of America. 100: 11361-6. PMID 12975528 DOI: 10.1073/pnas.2034878100  1
2003 England JL, Shakhnovich BE, Shakhnovich EI. Natural selection of more designable folds: a mechanism for thermophilic adaptation. Proceedings of the National Academy of Sciences of the United States of America. 100: 8727-31. PMID 12843403 DOI: 10.1073/pnas.1530713100  1
2003 Kussell E, Shimada J, Shakhnovich EI. Side-chain dynamics and protein folding. Proteins. 52: 303-21. PMID 12833553 DOI: 10.1002/prot.10426  1
2003 England JL, Shakhnovich EI. Structural determinant of protein designability. Physical Review Letters. 90: 218101. PMID 12786593 DOI: 10.1103/PhysRevLett.90.218101  1
2003 Chen W, Mirny L, Shakhnovich EI. Fold recognition with minimal gaps. Proteins. 51: 531-43. PMID 12784212 DOI: 10.1002/prot.10402  1
2003 Li L, Shakhnovich EI, Mirny LA. 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. 100: 4463-8. PMID 12679523 DOI: 10.1073/pnas.0737647100  1
2003 Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI. Functional fingerprints of folds: evidence for correlated structure-function evolution. Journal of Molecular Biology. 326: 1-9. PMID 12547186 DOI: 10.1016/S0022-2836(02)01362-1  1
2002 Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Direct molecular dynamics observation of protein folding transition state ensemble. Biophysical Journal. 83: 3525-32. PMID 12496119 DOI: 10.1016/S0006-3495(02)75352-6  1
2002 Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. Journal of Molecular Biology. 324: 851-7. PMID 12460582 DOI: 10.1016/S0022-2836(02)01112-9  1
2002 Kussell E, Shakhnovich EI. Glassy dynamics of side-chain ordering in a simple model of protein folding. Physical Review Letters. 89: 168101. PMID 12398757 DOI: 10.1103/PhysRevLett.89.168101  1
2002 Dokholyan NV, Shakhnovich B, Shakhnovich EI. Expanding protein universe and its origin from the biological Big Bang. Proceedings of the National Academy of Sciences of the United States of America. 99: 14132-6. PMID 12384571 DOI: 10.1073/pnas.202497999  1
2002 Mukamel EA, Shakhnovich EI. Phase diagram for unzipping DNA with long-range interactions. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 66: 032901. PMID 12366167 DOI: 10.1103/PhysRevE.66.032901  1
2002 Shimada J, Shakhnovich EI. 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. 99: 11175-80. PMID 12165568 DOI: 10.1073/pnas.162268099  1
2002 Dokholyan NV, Li L, Ding F, Shakhnovich EI. Topological determinants of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 99: 8637-41. PMID 12084924 DOI: 10.1073/pnas.122076099  1
2002 Ishchenko AV, Shakhnovich EI. SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. Journal of Medicinal Chemistry. 45: 2770-80. PMID 12061879 DOI: 10.1021/jm0105833  1
2002 Geissler PL, Shakhnovich EI. Reversible stretching of random heteropolymers. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 056110. PMID 12059650  1
2002 Borreguero JM, Dokholyan NV, Buldyrev SV, Shakhnovich EI, Stanley HE. Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. Journal of Molecular Biology. 318: 863-76. PMID 12054829 DOI: 10.1016/S0022-2836(02)00136-5  1
2002 Grzybowski BA, Ishchenko AV, Shimada J, Shakhnovich EI. From knowledge-based potentials to combinatorial lead design in silico. Accounts of Chemical Research. 35: 261-9. PMID 12020163 DOI: 10.1021/ar970146b  1
2002 Kussell E, Shimada J, Shakhnovich EI. 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. 99: 5343-8. PMID 11943859 DOI: 10.1073/pnas.072665799  1
2002 Grzybowski BA, Ishchenko AV, Kim CY, Topalov G, Chapman R, Christianson DW, Whitesides GM, Shakhnovich EI. Combinatorial computational method gives new picomolar ligands for a known enzyme. Proceedings of the National Academy of Sciences of the United States of America. 99: 1270-3. PMID 11818565 DOI: 10.1073/pnas.032673399  1
2002 Geissler PL, Shakhnovich EI. Reversible stretching of random heteropolymers Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 65: 056110/1-056110/4. DOI: 10.1103/PhysRevE.65.056110  1
2002 Geissler PL, Shakhnovich EI. Mechanical response of random heteropolymers Macromolecules. 35: 4429-4436. DOI: 10.1021/ma012008e  1
2002 Dokholyan NV, Mirny LA, Shakhnovich EI. Understanding conserved amino acids in proteins Physica a: Statistical Mechanics and Its Applications. 314: 600-606. DOI: 10.1016/S0378-4371(02)01079-8  1
2002 Shimada J, Ekins S, Elkin C, Shakhnovich EI, Wery JP. Integrating computer-based de novo drug design and multidimensional filtering for desirable drugs Drug Discovery Today: Targets. 1: 196-205.  1
2001 Tiana G, Broglia RA, Shakhnovich EI. Energy profile of the space of model protein sequences. Journal of Biological Physics. 27: 147-59. PMID 23345740 DOI: 10.1023/A:1013151530254  1
2001 Li L, Shakhnovich EI. 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. 98: 13014-8. PMID 11606790 DOI: 10.1073/pnas.241378398  1
2001 Dokholyan NV, Shakhnovich EI. Understanding hierarchical protein evolution from first principles. Journal of Molecular Biology. 312: 289-307. PMID 11545603 DOI: 10.1006/jmbi.2001.4949  1
2001 Kussell E, Shimada J, Shakhnovich EI. Excluded volume in protein side-chain packing. Journal of Molecular Biology. 311: 183-93. PMID 11469867 DOI: 10.1006/jmbi.2001.4846  1
2001 Berriz GF, Shakhnovich EI. Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model. Journal of Molecular Biology. 310: 673-85. PMID 11439031 DOI: 10.1006/jmbi.2001.4792  1
2001 Pitard E, Shakhnovich EI. Mode-coupling theory for heteropolymers. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 63: 041501. PMID 11308842 DOI: 10.1103/PhysRevE.63.041501  1
2001 Shimada J, Kussell EL, Shakhnovich EI. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. Journal of Molecular Biology. 308: 79-95. PMID 11302709 DOI: 10.1006/jmbi.2001.4586  1
2001 Li L, Shakhnovich EI. Different circular permutations produced different folding nuclei in proteins: a computational study. Journal of Molecular Biology. 306: 121-32. PMID 11178898 DOI: 10.1006/jmbi.2000.4375  1
2000 Wilder J, Shakhnovich EI. Proteins with selected sequences: a heteropolymeric study. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 62: 7100-10. PMID 11102067  1
2000 Choe SE, Li L, Matsudaira PT, Wagner G, Shakhnovich EI. Differential stabilization of two hydrophobic cores in the transition state of the villin 14T folding reaction. Journal of Molecular Biology. 304: 99-115. PMID 11071813 DOI: 10.1006/jmbi.2000.4190  1
2000 Vendruscolo M, Mirny LA, Shakhnovich EI, Domany E. Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score. Proteins. 41: 192-201. PMID 10966572 DOI: 10.1002/1097-0134(20001101)41:2<192::AID-PROT40>3.0.CO;2-3  1
2000 Mirny LA, Finkelstein AV, Shakhnovich EI. Statistical significance of protein structure prediction by threading. Proceedings of the National Academy of Sciences of the United States of America. 97: 9978-83. PMID 10954732 DOI: 10.1073/pnas.160271197  1
2000 Abkevich VI, Shakhnovich EI. What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis. Journal of Molecular Biology. 300: 975-85. PMID 10891282 DOI: 10.1006/jmbi.2000.3893  1
2000 Shimada J, Ishchenko AV, Shakhnovich EI. Analysis of knowledge-based protein-ligand potentials using a self-consistent method. Protein Science : a Publication of the Protein Society. 9: 765-75. PMID 10794420 DOI: 10.1110/ps.9.4.765  1
2000 Li L, Mirny LA, Shakhnovich EI. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nature Structural Biology. 7: 336-42. PMID 10742180 DOI: 10.1038/74111  1
2000 Tiana G, Broglia RA, Shakhnovich EI. Hiking in the energy landscape in sequence space: a bumpy road to good folders. Proteins. 39: 244-51. PMID 10737946 DOI: 10.1002/(SICI)1097-0134(20000515)39:3<244::AID-PROT70>3.0.CO;2-#  1
2000 Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Identifying the protein folding nucleus using molecular dynamics. Journal of Molecular Biology. 296: 1183-8. PMID 10698625 DOI: 10.1006/jmbi.1999.3534  1
2000 Grzybowski BA, Anderson JR, Colton I, Brittain ST, Shakhnovich EI, Whitesides GM. Modeling the kinetics of acylation of insulin using a recursive method for solving the systems of coupled differential equations. Biophysical Journal. 78: 652-61. PMID 10653778 DOI: 10.1016/S0006-3495(00)76623-9  1
2000 Grzybowski BA, Ishchenko AV, Dewitte RS, Whitesides GM, Shakhnovich EI. Development of a knowledge-based potential for crystals of small organic molecules: Calculation of energy surfaces for C=0⋯H-N hydrogen bonds Journal of Physical Chemistry B. 104: 7293-7298.  1
1999 Finkel'shteĭn AV, Rykunov DS, Lobanov MIu, Badretdinov FIa, Reva BA, Skolnick J, Mirnyĭ LA, Shakhnovich EI. [When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible]. Biofizika. 44: 980-91. PMID 10707272  1
1999 Morrissey MP, Shakhnovich EI. Evidence for the role of PrP(C) helix 1 in the hydrophilic seeding of prion aggregates. Proceedings of the National Academy of Sciences of the United States of America. 96: 11293-8. PMID 10500170 DOI: 10.1073/pnas.96.20.11293  1
1999 Mirny LA, Shakhnovich EI. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. Journal of Molecular Biology. 291: 177-96. PMID 10438614 DOI: 10.1006/jmbi.1999.2911  1
1999 Shakhnovich EI. Folding by association. Nature Structural Biology. 6: 99-102. PMID 10048934 DOI: 10.1038/5785  1
1999 Berriz GF, Shakhnovich EI. The well-tempered protein Current Opinion in Colloid and Interface Science. 4: 72-82. DOI: 10.1016/S1359-0294(99)00010-2  1
1999 DeWitte RS, Shakhnovich EI. SmoG: A ligand design method based on knowledge-based parametrization of a solvent reorganization model Acs Symposium Series. 719: 70-86.  1
1999 Finkelstein AV, Rykunov DS, Lobanov MY, Badretdinov AY, Reva BA, Skolnick J, Mirny LA, Shakhnovich EI. When and how the homologs can overcome errors in the energy estimates and make the 3D structure prediction possible Biofizika. 44: 990-991.  1
1999 Chou JJ, Shakhnovich EI. A study on local-global cooperativity in protein collapse Journal of Physical Chemistry B. 103: 2535-2542.  1
1999 Kussell EL, Shakhnovich EI. Analytical Approach to the Protein Design Problem Physical Review Letters. 83: 4437-4440.  1
1999 Qi S, Chakraborty AK, Wang H, Lefebvre AA, Balsara NP, Shakhnovich EI, Xenidou M, Hadjichristidis N. Microphase ordering in melts of randomly grafted copolymers Physical Review Letters. 82: 2896-2899.  1
1999 Roan JR, Shakhnovich EI. Phase separation of a binary fluid containing surfactants in a Hele-Shaw cell Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 59: 2109-2125.  1
1998 Shakhnovich EI. Folding nucleus: specific or multiple? Insights from lattice models and experiments. Folding & Design. 3: R108-11; discussion . PMID 9889170 DOI: 10.1016/S1359-0278(98)00056-X  1
1998 Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Discrete molecular dynamics studies of the folding of a protein-like model. Folding & Design. 3: 577-87. PMID 9889167 DOI: 10.1016/S1359-0278(98)00072-8  1
1998 Choe SE, Matsudaira PT, Osterhout J, Wagner G, Shakhnovich EI. Folding kinetics of villin 14T, a protein domain with a central beta-sheet and two hydrophobic cores. Biochemistry. 37: 14508-18. PMID 9772179 DOI: 10.1021/bi980889k  1
1998 Mirny LA, Shakhnovich EI. Protein structure prediction by threading. Why it works and why it does not. Journal of Molecular Biology. 283: 507-26. PMID 9769221 DOI: 10.1006/jmbi.1998.2092  1
1998 Shakhnovich EI. Protein design: a perspective from simple tractable models. Folding & Design. 3: R45-58. PMID 9669878 DOI: 10.1016/S1359-0278(98)00021-2  1
1998 Fersht AR, Shakhnovich EI. Protein folding: think globally, (inter)act locally. Current Biology : Cb. 8: R478-9. PMID 9663379  1
1998 Abkevich VI, Gutin AM, Shakhnovich EI. Theory of kinetic partitioning in protein folding with possible applications to prions. Proteins. 31: 335-44. PMID 9626694 DOI: 10.1002/(SICI)1097-0134(19980601)31:4<335::AID-PROT1>3.0.CO;2-H  1
1998 Gutin AM, Abkevich VI, Shakhnovich EI. A protein engineering analysis of the transition state for protein folding: simulation in the lattice model. Folding & Design. 3: 183-94. PMID 9562547 DOI: 10.1016/S1359-0278(98)00026-1  1
1998 Mirny LA, Abkevich VI, Shakhnovich EI. How evolution makes proteins fold quickly. Proceedings of the National Academy of Sciences of the United States of America. 95: 4976-81. PMID 9560213 DOI: 10.1073/pnas.95.9.4976  1
1998 Roan JR, Shakhnovich EI. Stability study of icosahedral phases in diblock copolymer melt Journal of Chemical Physics. 109: 7591-7611. DOI: 10.1063/1.477381  1
1998 Mammen M, Shakhnovich EI, Deutch JM, Whitesides GM. Estimating the Entropic Cost of Self-Assembly of Multiparticle Hydrogen-Bonded Aggregates Based on the Cyanuric Acid-Melamine Lattice Journal of Organic Chemistry. 63: 3821-3830.  1
1998 Mammen M, Shakhnovich EI, Whitesides GM. Using a Convenient, Quantitative Model for Torsional Entropy to Establish Qualitative Trends for Molecular Processes That Restrict Conformational Freedom Journal of Organic Chemistry. 63: 3168-3175.  1
1998 Gutin A, Sali A, Abkevich V, Karplus M, Shakhnovich EI. Temperature dependence of the folding rate in a simple protein model: Search for a "glass" transition Journal of Chemical Physics. 108: 6466-6483.  1
1998 Chakraborty AK, Shakhnovich EI, Pande VS. Freezing of compact random heteropolymers with correlated sequence fluctuations Journal of Chemical Physics. 108: 1683-1687.  1
1997 Abkevich VI, Gutin AM, Shakhnovich EI. Computer simulations of prebiotic evolution Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27-38. PMID 9390277  1
1997 Shakhnovich EI. Theoretical studies of protein-folding thermodynamics and kinetics Current Opinion in Structural Biology. 7: 29-40. PMID 9032061 DOI: 10.1016/S0959-440X(97)80005-X  1
1997 DeWitte RS, Ishchenko AV, Shakhnovich EI. SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 2. Case studies in molecular design Journal of the American Chemical Society. 119: 4608-4617. DOI: 10.1021/ja963689+  1
1997 Bratko D, Chakraborty AK, Shakhnovich EI. Recognition between random heteropolymers and multifunctional disordered surfaces Chemical Physics Letters. 280: 46-52.  1
1997 Sfatos CD, Shakhnovich EI. Statistical mechanics of random heteropolymers Physics Report. 288: 77-108.  1
1997 Berriz GF, Gutin AM, Shakhnovich EI. Cooperativity and stability in a Langevin model of proteinlike folding Journal of Chemical Physics. 106: 9276-9285.  1
1997 Bratko D, Chakraborty AK, Shakhnovich EI. The structure of a random heteropolymer in a disordered medium: Ensemble growth simulation Journal of Chemical Physics. 106: 1264-1279.  1
1996 Mirny LA, Abkevich V, Shakhnovich EI. Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model. Folding & Design. 1: 103-16. PMID 9079370 DOI: 10.1016/S1359-0278(96)00019-3  1
1996 Mirny LA, Shakhnovich EI. How to derive a protein folding potential? A new approach to an old problem. Journal of Molecular Biology. 264: 1164-79. PMID 9000638 DOI: 10.1006/jmbi.1996.0704  1
1996 Roan JR, Shakhnovich EI. Dynamics of heteropolymers in dilute solution: Effective equation of motion and relaxation spectrum Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 54: 5340-5357.  1
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