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For: Gao M, Skolnick J. iAlign: a method for the structural comparison of protein-protein interfaces. ACTA ACUST UNITED AC 2010;26:2259-65. [PMID: 20624782 DOI: 10.1093/bioinformatics/btq404] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Number Cited by Other Article(s)
51
Kuzu G, Gursoy A, Nussinov R, Keskin O. Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. J Proteome Res 2013;12:2641-53. [PMID: 23590674 PMCID: PMC3685852 DOI: 10.1021/pr400006k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
52
Jo S, Lee HS, Skolnick J, Im W. Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. PLoS Comput Biol 2013;9:e1002946. [PMID: 23516343 PMCID: PMC3597548 DOI: 10.1371/journal.pcbi.1002946] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/10/2013] [Indexed: 11/29/2022]  Open
53
Gao M, Skolnick J. APoc: large-scale identification of similar protein pockets. ACTA ACUST UNITED AC 2013;29:597-604. [PMID: 23335017 DOI: 10.1093/bioinformatics/btt024] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
54
Low-resolution structural modeling of protein interactome. Curr Opin Struct Biol 2013;23:198-205. [PMID: 23294579 DOI: 10.1016/j.sbi.2012.12.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 12/03/2012] [Indexed: 11/23/2022]
55
Sukhwal A, Sowdhamini R. Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies. MOLECULAR BIOSYSTEMS 2013;9:1652-61. [DOI: 10.1039/c3mb25484d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
56
Pang B, Kuang X, Zhao N, Korkin D, Shyu CR. PBSword: a web server for searching similar protein-protein binding sites. Nucleic Acids Res 2012;40:W428-34. [PMID: 22689645 PMCID: PMC3394332 DOI: 10.1093/nar/gks527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
57
Yang Y, Zhan J, Zhao H, Zhou Y. A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction. Proteins 2012;80:2080-8. [PMID: 22522696 DOI: 10.1002/prot.24100] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 04/13/2012] [Accepted: 04/17/2012] [Indexed: 11/12/2022]
58
Pang B, Zhao N, Korkin D, Shyu CR. Fast protein binding site comparisons using visual words representation. ACTA ACUST UNITED AC 2012;28:1345-52. [PMID: 22492639 DOI: 10.1093/bioinformatics/bts138] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
59
The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation. Proc Natl Acad Sci U S A 2012;109:3784-9. [PMID: 22355140 DOI: 10.1073/pnas.1117768109] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
60
Xie L, Xie L, Kinnings SL, Bourne PE. Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu Rev Pharmacol Toxicol 2011;52:361-79. [PMID: 22017683 DOI: 10.1146/annurev-pharmtox-010611-134630] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
61
Skolnick J, Zhou H, Brylinski M. Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function. Phys Chem Chem Phys 2011;13:17044-55. [PMID: 21655593 PMCID: PMC3289135 DOI: 10.1039/c1cp21140d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
62
Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW. Spatial clustering of protein binding sites for template based protein docking. Bioinformatics 2011;27:2820-7. [DOI: 10.1093/bioinformatics/btr493] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
63
Mehra-Chaudhary R, Mick J, Tanner JJ, Beamer LJ. Quaternary structure, conformational variability and global motions of phosphoglucosamine mutase. FEBS J 2011;278:3298-307. [PMID: 21767345 DOI: 10.1111/j.1742-4658.2011.08246.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
64
Shazman S, Elber G, Mandel-Gutfreund Y. From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces. Nucleic Acids Res 2011;39:7390-9. [PMID: 21693557 PMCID: PMC3177183 DOI: 10.1093/nar/gkr395] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
65
Tuncbag N, Gursoy A, Keskin O. Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces. Phys Biol 2011;8:035006. [PMID: 21572173 DOI: 10.1088/1478-3975/8/3/035006] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
66
Gao M, Skolnick J. New benchmark metrics for protein-protein docking methods. Proteins 2011;79:1623-34. [PMID: 21365685 PMCID: PMC3076516 DOI: 10.1002/prot.22987] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 12/22/2010] [Accepted: 12/30/2010] [Indexed: 11/10/2022]
67
Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proc Natl Acad Sci U S A 2010;107:22517-22. [PMID: 21149688 DOI: 10.1073/pnas.1012820107] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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