Predicting protein-protein interface residues using local surface structural similarity

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Jordan, Rafael A ^a,c   El Manzalawy, Yasser ^a,d   Dobbs, Drena ^b   Honavar, Vasant ^a,b  

^a Iowa State University   (United States)

^b IOWA STATE UNIVERSITY   (United States)

^c PONTIFICIA UNIVERSIDAD JAVERIANA   (Colombia)

^d Al Azhar University   (Egypt)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESSIBLE SURFACE AREAS; ATOMIC COMPOSITIONS; BENCHMARK DATASETS; DRUG DISCOVERY; EFFECTIVE APPROACHES; INTERFACE PREDICTION; INTERFACE RESIDUES; LOCAL SURFACES; PROTEIN SURFACE; PROTEIN-PROTEIN INTERACTIONS; PROTEIN-PROTEIN INTERFACE; QUERY PROTEINS; SIGNIFICANT IMPACTS; STRUCTURAL ELEMENTS; STRUCTURAL SIMILARITY; STRUCTURE-BASED; SURFACE RESIDUES; WEB SERVERS;

COMPOSITE STRUCTURES; FORECASTING;

PROTEINS;

PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; METABOLISM; PROTEIN CONFORMATION; PROTEIN DOMAIN;

ALGORITHMS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEINS; SOFTWARE;

EID: 84858175431     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-41     Document Type: Article

References (50)

1. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM. A protein interaction map of Drosophila melanogaster. Science 2003, 302(5651):1727-1736. 10.1126/science.1090289, 14605208.
2. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JDJ, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Heuvel SVD, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M. A map of the interactome network of the metazoan C. elegans. Science 2004, 303(5657):540-543. 10.1126/science.1091403, 1698949, 14704431.
3. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, Onge PS, Ghanny S, Lam MHY, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440(7084):637-643. 10.1038/nature04670, 16554755.
4. Yu J, Fotouhi F. Computational approaches for predicting protein-protein interactions: a survey. J Med Syst 2006, 30:39-44. 10.1007/s10916-006-7402-3, 16548413.
5. Li X, Wu M, Kwoh CK, Ng SK. Computational approaches for detecting protein complexes from protein interaction networks: a survey. BMC Genomics 2010, 11(1):S3. 10.1186/1471-2164-11-S1-S3, 3045796, 21210969.
6. Fernández-Recio J. Prediction of protein binding sites and hot spot. Wiley Interdisciplinary Reviews: Computational Molecular Science 2011,
7. 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(3):233-246.
8. Zhou HX, Qin S. Interaction-Site Prediction for Protein Complexes: a Critical Assessment. Bioinformatics 2007, 23:3386-3387. 10.1093/bioinformatics/btm434, 17895276.
9. de Vries SJ, Bonvin AMJJ. How proteins get in touch: interface prediction in the study of biomolecular complexes. Curr Protein Pept Sci 2008, 9(4):394-406. 10.2174/138920308785132712, 18691126.
10. Bartoli L, Martelli PL, Rossi I, Fariselli P, Casadio R. Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks. CMSB 09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology 2009, 1-17. Berlin: Springer-Verlag, Degano, Pierpaolo, Gorrieri, Roberto.
11. Nussinov R. Computational protein-protein interactions 2009, CRC.
12. 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(3):217-232. 2671387, 19240123.
13. Fariselli P, Pazos F, Valencia A, Casadio R. Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 2002, 269(5):1356-1361. 10.1046/j.1432-1033.2002.02767.x, 11874449.
14. Yan C, Dobbs D, Honavar V. A two-stage classifier for identification of protein-protein interface residues. Bioinformatics 2004, 20(Suppl 1):i371-i378. 10.1093/bioinformatics/bth920, 15262822.
15. Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005, 21(8):1487-1494. 10.1093/bioinformatics/bti242, 15613384.
16. Wu F, Olson B, Dobbs D, Honavar V. Comparing Kernels For Predicting Protein Binding Sites From Amino Acid Sequenc. IEEE Joint Conference on Neural Networks 2006, Vancouver, Canada: IEEE Press.
17. Chung JL, Wang W, Bourne PE. High-throughput identification of interacting protein-protein binding sites. BMC Bioinforma 2007, 8:223.
18. Ofran Y, Rost B. ISIS: interaction sites identified from sequence. Bioinformatics 2007, 23(2):e13-e16. 10.1093/bioinformatics/btl303, 17237081.
19. Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins: Struct, Funct and Bioinf 2007, 66(3):630-645.
20. 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 Bioinforma 2009, 10:381.
21. Sikić M, Tomić S, Vlahovicek K. Prediction of protein-protein interaction sites in sequences and 3D structures by random forests. PLoS Comput Biol 2009, 5:e1000278. 10.1371/journal.pcbi.1000278, 2621338, 19180183.
22. Liu R, Jiang W, Zhou Y. Identifying protein-protein interaction sites in transient complexes with temperature factor, sequence profile and accessible surface area. Amino Acids 2010, 38:263-270. 10.1007/s00726-009-0245-8, 19214704.
23. Murakami Y, Mizuguchi K. Applying the Naive Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites. Bioinformatics 2010, 26(15):1841-1848. 10.1093/bioinformatics/btq302, 20529890.
24. Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 1997, 272:133-143. 10.1006/jmbi.1997.1233, 9299343.
25. Neuvirth H, Raz R, Schreiber G. ProMate: A Structure Based Prediction Program to Identify the Location of Protein-Protein Binding Sites. J Mol Biol 2004, 338:181-199. 10.1016/j.jmb.2004.02.040, 15050833.
26. Rossi A, Marti-Renom MA, Sali A. Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Sci 2006, 15(10):2366-2380. 10.1110/ps.062247506, 2242385, 16963645.
27. Jones S, Mukarami Y. Patch Prediction of Protein Interaction Sites: Validation of a Scoring Function for an Online Server. Bioinformatics Research and Development 2007, 4414:303-313.
28. Naveed H, Jackups R, Liang J. Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins. Proc Natl Acad Sci USA 2009, 106(31):12735-12740. 10.1073/pnas.0902169106, 2722334, 19622743.
29. Shoemaker BA, Zhang D, Thangudu RR, Tyagi M, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR. Inferred Biomolecular Interaction Server-a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res 2010, 38(Database):D518-D524. 10.1093/nar/gkp842, 2808861, 19843613.
30. Ma B, Elkayam T, Wolfson H, Nussinov R. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci USA 2003, 100(10):5772-5777. 10.1073/pnas.1030237100, 156276, 12730379.
31. Chung JL, Wang W, Bourne PE. Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins 2006, 62(3):630-640.
32. Tuncbag N, Gursoy A, Guney E, Nussinov R, Keskin O. Architectures and functional coverage of protein-protein interfaces. J Mol Biol 2008, 381(3):785-802. 10.1016/j.jmb.2008.04.071, 2605427, 18620705.
33. Dayhoff JE, Shoemaker BA, Bryant SH, Panchenko AR. Evolution of protein binding modes in homooligomers. J Mol Biol 2010, 395(4):860-870. 10.1016/j.jmb.2009.10.052, 2813322, 19879880.
34. Guharoy M, Chakrabarti P. Conserved residue clusters at protein-protein interfaces and their use in binding site identification. BMC Bioinforma 2010, 11:286.
35. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
36. Konc J, Janežič D. Protein-protein binding-sites prediction by protein surface structure conservation. J Chem Inf Model 2007, 47(3):940-944. 10.1021/ci6005257, 17388583.
37. Carl N, Konc J, Janežič D. Protein surface conservation in binding sites. J Chem Inf Model 2008, 48(6):1279-1286. 10.1021/ci8000315, 18476685.
38. Zhang QC, Petrey D, Norel R, Honig BH. Protein interface conservation across structure space. Proc Natl Acad Sci USA 2010, 107(24):10896-10901. 10.1073/pnas.1005894107, 2890749, 20534496.
39. Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res 2011, 39:W283-W287. 10.1093/nar/gkr311, 3125747, 21609948.
40. Konc J, Janežič D. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics 2010, 26(9):1160-1168. 10.1093/bioinformatics/btq100, 2859123, 20305268.
41. Carl N, Konc J, Vehar B, Janežič D. Protein-Protein Binding Site Prediction by Local Structural Alignment. J Chem Inf Model 2010, 50(10):1906-1913. 10.1021/ci100265x, 20919700.
42. Hubbard S, Thornton J. NACCESS, Computer Program, Department of Biochemistry and Molecular Biology. 1993, University College London., http://www.bioinf.manchester.ac.uk/naccess/
43. Jordan RA, Wu F, Dobbs D, Honavar V. ProtinDb: A data base of protein-protein interface residues. 2011, Iowa State University., http://protindb.cs.iastate.edu/
44. Henrick K, Thornton J. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998, 23(9):358. 10.1016/S0968-0004(98)01253-5, 9787643.
45. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins 2008, 73(3):705-709. 10.1002/prot.22106, 2726780, 18491384.
46. Janin J, Wodak S. The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007. Structure 2007, 15(7):755-759. 10.1016/j.str.2007.06.007, 17637336.
47. Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000, 16(5):412-424. 10.1093/bioinformatics/16.5.412, 10871264.
48. Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucl Acids Res 2006, 34(13):3698-3707. 10.1093/nar/gkl454, 1540721, 16893954.
49. Chen H, Zhou HX. Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data. Proteins: Struct Funct Bioinf 2005, 61:21-35.
50. Qin S, Zhou HX. Meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformatics 2007, 23(24):3386-3387. 10.1093/bioinformatics/btm434, 17895276.