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For: Ofran Y, Rost B. ISIS: interaction sites identified from sequence. Bioinformatics 2007;23:e13-6. [PMID: 17237081 DOI: 10.1093/bioinformatics/btl303] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
151
Mészáros B, Simon I, Dosztányi Z. The expanding view of protein-protein interactions: complexes involving intrinsically disordered proteins. Phys Biol 2011;8:035003. [PMID: 21572179 DOI: 10.1088/1478-3975/8/3/035003] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
152
Fernández‐Recio J. Prediction of protein binding sites and hot spots. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.45] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
153
Chennamsetty N, Voynov V, Kayser V, Helk B, Trout BL. Prediction of protein binding regions. Proteins 2010;79:888-97. [DOI: 10.1002/prot.22926] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 09/23/2010] [Accepted: 10/13/2010] [Indexed: 11/07/2022]
154
Lateral acquisition of genes is affected by the friendliness of their products. Proc Natl Acad Sci U S A 2010;108:343-8. [PMID: 21149709 DOI: 10.1073/pnas.1009775108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
155
Chen P, Li J. Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information. BMC Bioinformatics 2010;11:402. [PMID: 20667087 PMCID: PMC2921408 DOI: 10.1186/1471-2105-11-402] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 07/28/2010] [Indexed: 01/09/2023]  Open
156
Murakami Y, Mizuguchi K. Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites. ACTA ACUST UNITED AC 2010;26:1841-8. [PMID: 20529890 DOI: 10.1093/bioinformatics/btq302] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
157
Ozbek P, Soner S, Erman B, Haliloglu T. DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. Nucleic Acids Res 2010;38:W417-23. [PMID: 20478828 PMCID: PMC2896127 DOI: 10.1093/nar/gkq396] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
158
Gromiha MM, Yokota K, Fukui K. Energy based approach for understanding the recognition mechanism in protein-protein complexes. MOLECULAR BIOSYSTEMS 2010;5:1779-86. [PMID: 19593470 DOI: 10.1039/b904161n] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
159
Identification and Analysis of Binding Site Residues in Protein Complexes: Energy Based Approach. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/978-3-642-14922-1_78] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
160
Gromiha MM, Yokota K, Fukui K. Sequence and structural analysis of binding site residues in protein-protein complexes. Int J Biol Macromol 2009;46:187-92. [PMID: 20026105 DOI: 10.1016/j.ijbiomac.2009.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/23/2009] [Accepted: 11/24/2009] [Indexed: 12/24/2022]
161
Dosztanyi Z, Meszaros B, Simon I. Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins. Brief Bioinform 2009;11:225-43. [DOI: 10.1093/bib/bbp061] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
162
Liu B, Wang X, Lin L, Tang B, Dong Q, Wang X. Prediction of protein binding sites in protein structures using hidden Markov support vector machine. BMC Bioinformatics 2009;10:381. [PMID: 19925685 PMCID: PMC2785799 DOI: 10.1186/1471-2105-10-381] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2009] [Accepted: 11/20/2009] [Indexed: 01/08/2023]  Open
163
Using Support Vector Machine Combined with Post-processing Procedure to Improve Prediction of Interface Residues in Transient Complexes. Protein J 2009;28:369-74. [DOI: 10.1007/s10930-009-9203-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
164
Hu J, Yan C. A tool for calculating binding-site residues on proteins from PDB structures. BMC STRUCTURAL BIOLOGY 2009;9:52. [PMID: 19650927 PMCID: PMC2728722 DOI: 10.1186/1472-6807-9-52] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Accepted: 08/03/2009] [Indexed: 11/24/2022]
165
Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML. Progress and challenges in predicting protein-protein interaction sites. Brief Bioinform 2009;10:233-46. [PMID: 19346321 DOI: 10.1093/bib/bbp021] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
166
Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R. A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform 2009;10:217-32. [PMID: 19240123 DOI: 10.1093/bib/bbp001] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
167
Wrzeszczynski KO, Rost B. Cell cycle kinases predicted from conserved biophysical properties. Proteins 2009;74:655-68. [PMID: 18704950 PMCID: PMC2629806 DOI: 10.1002/prot.22181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
168
Prediction of protein-protein interaction sites in sequences and 3D structures by random forests. PLoS Comput Biol 2009;5:e1000278. [PMID: 19180183 PMCID: PMC2621338 DOI: 10.1371/journal.pcbi.1000278] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 12/16/2008] [Indexed: 11/19/2022]  Open
169
Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A. Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling. PLoS Comput Biol 2009;5:e1000267. [PMID: 19165315 PMCID: PMC2613531 DOI: 10.1371/journal.pcbi.1000267] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 12/04/2008] [Indexed: 11/18/2022]  Open
170
A heterospecific leucine zipper tetramer. ACTA ACUST UNITED AC 2008;15:908-19. [PMID: 18804028 PMCID: PMC7111190 DOI: 10.1016/j.chembiol.2008.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 07/07/2008] [Accepted: 07/10/2008] [Indexed: 11/21/2022]
171
Protein–protein interaction and quaternary structure. Q Rev Biophys 2008;41:133-80. [PMID: 18812015 DOI: 10.1017/s0033583508004708] [Citation(s) in RCA: 301] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
172
Bromberg Y, Rost B. Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics 2008;24:i207-12. [PMID: 18689826 PMCID: PMC2597370 DOI: 10.1093/bioinformatics/btn268] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
173
Ming D, Cohn JD, Wall ME. Fast dynamics perturbation analysis for prediction of protein functional sites. BMC STRUCTURAL BIOLOGY 2008;8:5. [PMID: 18234095 PMCID: PMC2276503 DOI: 10.1186/1472-6807-8-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Accepted: 01/30/2008] [Indexed: 11/10/2022]
174
Ofran Y, Mysore V, Rost B. Prediction of DNA-binding residues from sequence. ACTA ACUST UNITED AC 2007;23:i347-53. [PMID: 17646316 DOI: 10.1093/bioinformatics/btm174] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
175
Ofran Y, Rost B. Protein-protein interaction hotspots carved into sequences. PLoS Comput Biol 2007;3:e119. [PMID: 17630824 PMCID: PMC1914369 DOI: 10.1371/journal.pcbi.0030119] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 05/11/2007] [Indexed: 11/24/2022]  Open
176
Bromberg Y, Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res 2007;35:3823-35. [PMID: 17526529 PMCID: PMC1920242 DOI: 10.1093/nar/gkm238] [Citation(s) in RCA: 667] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
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