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76
Deeds EJ, Shakhnovich EI. A structure-centric view of protein evolution, design, and adaptation. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2010;75:133-91, xi-xii. [PMID: 17124867 DOI: 10.1002/9780471224464.ch2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
77
Choi PJ, Xie XS, Shakhnovich EI. Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps. J Mol Biol 2009;396:230-44. [PMID: 19931280 DOI: 10.1016/j.jmb.2009.11.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 11/09/2009] [Accepted: 11/13/2009] [Indexed: 10/20/2022]
78
Kosmrlj A, Chakraborty AK, Kardar M, Shakhnovich EI. Thymic selection of T-cell receptors as an extreme value problem. PHYSICAL REVIEW LETTERS 2009;103:068103. [PMID: 19792616 DOI: 10.1103/physrevlett.103.068103] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Indexed: 05/28/2023]
79
Kutchukian PS, Yang JS, Verdine GL, Shakhnovich EI. All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples. J Am Chem Soc 2009;131:4622-7. [PMID: 19334772 DOI: 10.1021/ja805037p] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
80
Kutchukian PS, Lou D, Shakhnovich EI. FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space. J Chem Inf Model 2009;49:1630-42. [DOI: 10.1021/ci9000458] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
81
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 2009;79:051923. [PMID: 19518496 DOI: 10.1103/physreve.79.051923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2007] [Revised: 12/07/2008] [Indexed: 05/27/2023]
82
Zhang J, Shakhnovich EI. Slowly replicating lytic viruses: pseudolysogenic persistence and within-host competition. PHYSICAL REVIEW LETTERS 2009;102:178103. [PMID: 19518838 DOI: 10.1103/physrevlett.102.178103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Indexed: 05/27/2023]
83
Faísca PFN, Travasso RDM, Ball RC, Shakhnovich EI. Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis. J Chem Phys 2009;129:095108. [PMID: 19044896 DOI: 10.1063/1.2973624] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
84
Donald JE, Shakhnovich EI. SDR: a database of predicted specificity-determining residues in proteins. Nucleic Acids Res 2008;37:D191-4. [PMID: 18927118 PMCID: PMC2686543 DOI: 10.1093/nar/gkn716] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
85
Zhang J, Shakhnovich EI. Sensitivity-dependent model of protein-protein interaction networks. Phys Biol 2008;5:036011. [PMID: 18824789 DOI: 10.1088/1478-3975/5/3/036011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
86
Zhang J, Maslov S, Shakhnovich EI. Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Mol Syst Biol 2008;4:210. [PMID: 18682700 PMCID: PMC2538908 DOI: 10.1038/msb.2008.48] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 06/21/2008] [Indexed: 12/21/2022]  Open
87
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 Comput Biol 2008;3:e139. [PMID: 17630830 PMCID: PMC1914367 DOI: 10.1371/journal.pcbi.0030139] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 06/04/2007] [Indexed: 11/19/2022]  Open
88
Zeldovich KB, Shakhnovich EI. Understanding protein evolution: from protein physics to Darwinian selection. Annu Rev Phys Chem 2008;59:105-27. [PMID: 17937598 DOI: 10.1146/annurev.physchem.58.032806.104449] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
89
Shakhnovich BE, Shakhnovich EI. Improvisation in evolution of genes and genomes: whose structure is it anyway? Curr Opin Struct Biol 2008;18:375-81. [PMID: 18487041 DOI: 10.1016/j.sbi.2008.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Accepted: 02/13/2008] [Indexed: 01/31/2023]
90
Pereira de Araújo AF, Gomes ALC, 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 2008;70:971-83. [PMID: 17847091 DOI: 10.1002/prot.21571] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
91
Lukatsky DB, Shakhnovich EI. Statistically enhanced promiscuity of structurally correlated patterns. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008;77:020901. [PMID: 18351980 DOI: 10.1103/physreve.77.020901] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2007] [Indexed: 05/26/2023]
92
Zeldovich KB, Chen P, Shakhnovich EI. Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci U S A 2007;104:16152-7. [PMID: 17913881 PMCID: PMC2042177 DOI: 10.1073/pnas.0705366104] [Citation(s) in RCA: 187] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Indexed: 01/18/2023]  Open
93
Deeds EJ, Ashenberg O, Gerardin J, Shakhnovich EI. Robust protein protein interactions in crowded cellular environments. Proc Natl Acad Sci U S A 2007;104:14952-7. [PMID: 17848524 PMCID: PMC1986594 DOI: 10.1073/pnas.0702766104] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
94
Perlstein EO, Deeds EJ, Ashenberg O, Shakhnovich EI, Schreiber SL. Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations. Proc Natl Acad Sci U S A 2007;104:10553-8. [PMID: 17566105 PMCID: PMC1965551 DOI: 10.1073/pnas.0704037104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
95
Yang JS, Chen WW, Skolnick J, Shakhnovich EI. All-atom ab initio folding of a diverse set of proteins. Structure 2007;15:53-63. [PMID: 17223532 DOI: 10.1016/j.str.2006.11.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Revised: 11/15/2006] [Accepted: 11/18/2006] [Indexed: 11/30/2022]
96
Gomes ALC, de Rezende JR, Pereira de Araújo AF, Shakhnovich EI. Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions. Proteins 2007;66:304-20. [PMID: 17109406 DOI: 10.1002/prot.21137] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
97
Wallin S, Zeldovich KB, Shakhnovich EI. The folding mechanics of a knotted protein. J Mol Biol 2007;368:884-93. [PMID: 17368671 PMCID: PMC2692925 DOI: 10.1016/j.jmb.2007.02.035] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 02/07/2007] [Accepted: 02/09/2007] [Indexed: 11/18/2022]
98
Chen WW, Yang JS, Shakhnovich EI. A knowledge-based move set for protein folding. Proteins 2007;66:682-8. [PMID: 17143895 DOI: 10.1002/prot.21237] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
99
Berezovsky IN, Zeldovich KB, Shakhnovich EI. Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput Biol 2007;3:e52. [PMID: 17381236 PMCID: PMC1829478 DOI: 10.1371/journal.pcbi.0030052] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Accepted: 01/31/2007] [Indexed: 11/18/2022]  Open
100
Donald JE, Chen WW, Shakhnovich EI. Energetics of protein-DNA interactions. Nucleic Acids Res 2007;35:1039-47. [PMID: 17259221 PMCID: PMC1851630 DOI: 10.1093/nar/gkl1103] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
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