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For: Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res 2005;15:385-92. [PMID: 15741509 PMCID: PMC551565 DOI: 10.1101/gr.3133605] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Accepted: 11/23/2004] [Indexed: 11/24/2022]
Number Cited by Other Article(s)
1
Hollmann F, Sanchis J, Reetz MT. Learning from Protein Engineering by Deconvolution of Multi-Mutational Variants. Angew Chem Int Ed Engl 2024;63:e202404880. [PMID: 38884594 DOI: 10.1002/anie.202404880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024]
2
Middendorf L, Ravi Iyengar B, Eicholt LA. Sequence, Structure, and Functional Space of Drosophila De Novo Proteins. Genome Biol Evol 2024;16:evae176. [PMID: 39212966 PMCID: PMC11363682 DOI: 10.1093/gbe/evae176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/04/2024]  Open
3
Arpita K, Sharma S, Srivastava H, Kumar K, Mushtaq M, Gupta P, Jain R, Gaikwad K. Genome-wide survey, molecular evolution and expression analysis of Auxin Response Factor (ARF) gene family indicating their key role in seed number per pod in pigeonpea (C. cajan L. Millsp.). Int J Biol Macromol 2023;253:126833. [PMID: 37709218 DOI: 10.1016/j.ijbiomac.2023.126833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/26/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
4
Dubreuil B, Levy ED. Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins. Front Mol Biosci 2021;8:626729. [PMID: 33996892 PMCID: PMC8119896 DOI: 10.3389/fmolb.2021.626729] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/29/2021] [Indexed: 12/02/2022]  Open
5
Spence MA, Mortimer MD, Buckle AM, Minh BQ, Jackson CJ. A Comprehensive Phylogenetic Analysis of the Serpin Superfamily. Mol Biol Evol 2021;38:2915-2929. [PMID: 33744972 PMCID: PMC8233489 DOI: 10.1093/molbev/msab081] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
6
Auslander N, Gussow AB, Koonin EV. Incorporating Machine Learning into Established Bioinformatics Frameworks. Int J Mol Sci 2021;22:2903. [PMID: 33809353 PMCID: PMC8000113 DOI: 10.3390/ijms22062903] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 12/23/2022]  Open
7
Structure and function of naturally evolved de novo proteins. Curr Opin Struct Biol 2021;68:175-183. [PMID: 33567396 DOI: 10.1016/j.sbi.2020.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 01/05/2023]
8
Cambridge SB. Hypothesis: protein and RNA attributes are continuously optimized over time. BMC Genomics 2019;20:1012. [PMID: 31870287 PMCID: PMC6929361 DOI: 10.1186/s12864-019-6371-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 12/05/2019] [Indexed: 02/01/2023]  Open
9
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 2018;34:3557-3565. [PMID: 29741573 PMCID: PMC6184454 DOI: 10.1093/bioinformatics/bty370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/27/2018] [Accepted: 05/03/2018] [Indexed: 01/27/2023]  Open
10
Lacombe-Harvey MÈ, Brzezinski R, Beaulieu C. Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution. Appl Microbiol Biotechnol 2018;102:7219-7230. [PMID: 29931600 PMCID: PMC6097792 DOI: 10.1007/s00253-018-9149-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 12/20/2022]
11
Schiffrin B, Brockwell DJ, Radford SE. Outer membrane protein folding from an energy landscape perspective. BMC Biol 2017;15:123. [PMID: 29268734 PMCID: PMC5740924 DOI: 10.1186/s12915-017-0464-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
12
Williams PD, Pollock DD, Goldstein RA. Functionality and the Evolution of Marginal Stability in Proteins: Inferences from Lattice Simulations. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
13
Tian P, Best RB. How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis. Biophys J 2017;113:1719-1730. [PMID: 29045866 PMCID: PMC5647607 DOI: 10.1016/j.bpj.2017.08.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 12/23/2022]  Open
14
The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution. Biophys J 2017;112:1350-1365. [PMID: 28402878 DOI: 10.1016/j.bpj.2017.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 02/05/2023]  Open
15
Abrusán G, Marsh JA. Alpha Helices Are More Robust to Mutations than Beta Strands. PLoS Comput Biol 2016;12:e1005242. [PMID: 27935949 PMCID: PMC5147804 DOI: 10.1371/journal.pcbi.1005242] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/08/2016] [Indexed: 12/30/2022]  Open
16
Echave J, Spielman SJ, Wilke CO. Causes of evolutionary rate variation among protein sites. Nat Rev Genet 2016;17:109-21. [PMID: 26781812 DOI: 10.1038/nrg.2015.18] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
17
Sammond DW, Kastelowitz N, Himmel ME, Yin H, Crowley MF, Bomble YJ. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms. PLoS One 2016;11:e0145848. [PMID: 26741367 PMCID: PMC4704809 DOI: 10.1371/journal.pone.0145848] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022]  Open
18
Tóth-Petróczy A, Tawfik DS. The robustness and innovability of protein folds. Curr Opin Struct Biol 2014;26:131-8. [PMID: 25038399 DOI: 10.1016/j.sbi.2014.06.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 11/30/2022]
19
Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics. Curr Opin Struct Biol 2014;26:84-91. [PMID: 24952216 DOI: 10.1016/j.sbi.2014.05.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/19/2014] [Accepted: 05/16/2014] [Indexed: 11/24/2022]
20
Waldispühl J, O'Donnell CW, Will S, Devadas S, Backofen R, Berger B. Simultaneous alignment and folding of protein sequences. J Comput Biol 2014;21:477-91. [PMID: 24766258 DOI: 10.1089/cmb.2013.0163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
21
Zhang X, Perica T, Teichmann SA. Evolution of protein structures and interactions from the perspective of residue contact networks. Curr Opin Struct Biol 2013;23:954-63. [DOI: 10.1016/j.sbi.2013.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 10/26/2022]
22
Mannige RV. Two modes of protein sequence evolution and their compositional dependencies. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013;87:062714. [PMID: 23848722 DOI: 10.1103/physreve.87.062714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/10/2013] [Indexed: 06/02/2023]
23
Mohanty S, Purwar M, Srinivasan N, Rekha N. Tethering preferences of domain families co-occurring in multi-domain proteins. MOLECULAR BIOSYSTEMS 2013;9:1708-25. [PMID: 23571467 DOI: 10.1039/c3mb25481j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
24
Dellus-Gur E, Toth-Petroczy A, Elias M, Tawfik DS. What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs. J Mol Biol 2013;425:2609-21. [PMID: 23542341 DOI: 10.1016/j.jmb.2013.03.033] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 03/18/2013] [Accepted: 03/24/2013] [Indexed: 12/30/2022]
25
Micheletti C. Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments. Phys Life Rev 2012. [PMID: 23199577 DOI: 10.1016/j.plrev.2012.10.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
26
Li Y, Fang J. PROTS-RF: a robust model for predicting mutation-induced protein stability changes. PLoS One 2012;7:e47247. [PMID: 23077576 PMCID: PMC3471942 DOI: 10.1371/journal.pone.0047247] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 09/11/2012] [Indexed: 11/19/2022]  Open
27
Rorick M. Quantifying protein modularity and evolvability: a comparison of different techniques. Biosystems 2012;110:22-33. [PMID: 22796584 DOI: 10.1016/j.biosystems.2012.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 06/20/2012] [Accepted: 06/27/2012] [Indexed: 10/28/2022]
28
Hogeweg P. Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012;751:195-224. [PMID: 22821460 DOI: 10.1007/978-1-4614-3567-9_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
29
The evolution of protein structures and structural ensembles under functional constraint. Genes (Basel) 2011;2:748-62. [PMID: 24710290 PMCID: PMC3927589 DOI: 10.3390/genes2040748] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 10/15/2011] [Accepted: 10/19/2011] [Indexed: 02/06/2023]  Open
30
Rorick MM, Wagner GP. Protein structural modularity and robustness are associated with evolvability. Genome Biol Evol 2011;3:456-75. [PMID: 21602570 PMCID: PMC3134980 DOI: 10.1093/gbe/evr046] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
31
The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics 2011;188:479-88. [PMID: 21467571 DOI: 10.1534/genetics.111.128025] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
32
Systematic assessment of accuracy of comparative model of proteins belonging to different structural fold classes. J Mol Model 2011;17:2831-7. [PMID: 21301906 DOI: 10.1007/s00894-011-0976-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 01/17/2011] [Indexed: 10/18/2022]
33
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]
34
Influence of Conformational Entropy on the Protein Folding Rate. ENTROPY 2010. [DOI: 10.3390/e12040961] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
35
Kleinman CL, Rodrigue N, Lartillot N, Philippe H. Statistical potentials for improved structurally constrained evolutionary models. Mol Biol Evol 2010;27:1546-60. [PMID: 20159780 DOI: 10.1093/molbev/msq047] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
36
Covariation of branch lengths in phylogenies of functionally related genes. PLoS One 2009;4:e8487. [PMID: 20041191 PMCID: PMC2793527 DOI: 10.1371/journal.pone.0008487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 11/25/2009] [Indexed: 12/05/2022]  Open
37
Lan T, Yang ZL, Yang X, Liu YJ, Wang XR, Zeng QY. Extensive functional diversification of the Populus glutathione S-transferase supergene family. THE PLANT CELL 2009;21:3749-66. [PMID: 19996377 PMCID: PMC2814494 DOI: 10.1105/tpc.109.070219] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 10/31/2009] [Accepted: 11/16/2009] [Indexed: 05/17/2023]
38
Liu X, Zhao YP. Donut-shaped fingerprint in homologous polypeptide relationships--a topological feature related to pathogenic structural changes in conformational disease. J Theor Biol 2009;258:294-301. [PMID: 19248793 PMCID: PMC7094133 DOI: 10.1016/j.jtbi.2009.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 01/06/2009] [Accepted: 02/11/2009] [Indexed: 02/05/2023]
39
Trifonov EN, Frenkel ZM. Evolution of protein modularity. Curr Opin Struct Biol 2009;19:335-40. [PMID: 19386484 DOI: 10.1016/j.sbi.2009.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 03/16/2009] [Indexed: 10/20/2022]
40
Gu J, Hilser VJ. Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome. Structure 2009;16:1627-37. [PMID: 19000815 DOI: 10.1016/j.str.2008.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 08/07/2008] [Accepted: 08/19/2008] [Indexed: 11/30/2022]
41
Wagner A. Neutralism and selectionism: a network-based reconciliation. Nat Rev Genet 2008;9:965-74. [PMID: 18957969 DOI: 10.1038/nrg2473] [Citation(s) in RCA: 186] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
42
Peto M, Kloczkowski A, Honavar V, Jernigan RL. Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable. BMC Bioinformatics 2008;9:487. [PMID: 19014713 PMCID: PMC2655094 DOI: 10.1186/1471-2105-9-487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2008] [Accepted: 11/18/2008] [Indexed: 11/10/2022]  Open
43
Ferrada E, Wagner A. Protein robustness promotes evolutionary innovations on large evolutionary time-scales. Proc Biol Sci 2008;275:1595-602. [PMID: 18430649 DOI: 10.1098/rspb.2007.1617] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
44
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
45
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]
46
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]
47
Goldstein RA. The structure of protein evolution and the evolution of protein structure. Curr Opin Struct Biol 2008;18:170-7. [DOI: 10.1016/j.sbi.2008.01.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 12/20/2007] [Accepted: 01/09/2008] [Indexed: 11/29/2022]
48
Zhou T, Drummond DA, Wilke CO. Contact density affects protein evolutionary rate from bacteria to animals. J Mol Evol 2008;66:395-404. [PMID: 18379715 DOI: 10.1007/s00239-008-9094-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 02/16/2008] [Accepted: 02/25/2008] [Indexed: 12/29/2022]
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Wong P, Frishman D. Designability and disease. Methods Mol Biol 2008;484:491-504. [PMID: 18592197 DOI: 10.1007/978-1-59745-398-1_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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Galzitskaya OV, Reifsnyder DC, Bogatyreva NS, Ivankov DN, Garbuzynskiy SO. More compact protein globules exhibit slower folding rates. Proteins 2007;70:329-32. [PMID: 17876831 DOI: 10.1002/prot.21619] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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