Prediction of protein-protein binding site by using core interface residue and support vector machine

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Li, Nan ^a,b   Sun, Zhonghua ^a,b   Jiang, Fan ^a  

^a INSTITUTE OF PHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITE PREDICTIONS; BIOLOGICAL APPLICATIONS; PHYSICAL AND CHEMICAL CHARACTERISTICS; PROTEIN INTERACTION; PROTEIN INTERACTION SITES; PROTEIN-PROTEIN BINDING; PROTEIN-PROTEIN INTERACTIONS; SURROUNDING ENVIRONMENT;

BIOCHEMISTRY; FORECASTING; MOLECULAR BIOLOGY; SUPPORT VECTOR MACHINES;

PROTEINS;

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; BIOLOGICAL MODEL; COMPUTER PROGRAM; GENETICS; METABOLISM; METHODOLOGY; PROTEIN BINDING; PROTEOMICS; SENSITIVITY AND SPECIFICITY;

AMINO ACID SEQUENCE; BINDING SITES; MODELS, GENETIC; PROTEIN BINDING; PROTEINS; PROTEOMICS; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 61449091497     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-553     Document Type: Article

References (51)

1. van Dijk ADJ Boelens R Bonvin AMJJ: Data-driven docking for the study of biomolecular complexes. FEBS Journal 2005, 272:293-312. 10.1111/ j.1742-4658.2004.04473.x 15654870
2. Krogan NJ Cagney G Yu H Zhong G Guo X Ignatchenko A Li J Pu S Datta N Tikuisis AP Punna T Peregrin-Alvarez JM Shales M Zhang X Davery 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 SR Onge PS Ghanny S Lam MH Butland G Altaf-Ul AM Kanaya S Shilatifard A O'Shea Weissman JS Ingles CJ Heghes TR Parkinson J Gerstein M Wodak SJ Emili A Greenblatt JF: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440:637-643. 10.1038/ nature04670 16554755
3. Phizicky E Bastiaens PI Zhu H Snyder M Fields S: Protein analysis on a proteomic scale. Nature 2003, 422:208-215. 10.1038/nature01512 12634794
4. Smith JR Sternberg MJ: Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002, 12:28-35. 10.1016/ S0959-440X(02)00285-3 11839486
5. Lensink MF Mendez R Wodak SJ: Docking and scoring protein complexes: CAPRI 3rd edition. Proteins 2007, 69:704-718. 10.1002/prot.21804 17918726
6. Smith GR Fitzjohn PW Page CS Bates PA: Incorporation of flexibility into rigid-body docking: Applications in rounds 3-5 of CAPRI. Proteins 2005, 60:263-268. 10.1002/prot.20568 15981258
7. Qin S Zhou HX: A holistic approach to protein docking. Proteins 2007, 69:743-749. 10.1002/prot.21752 17803232
8. Lo Conte L Chothia C Janin J: The atomic structure of protein-protein recognition sites. J Mol Biol 1999, 285:2177-2198. 10.1006/ jmbi.1998.2439 9925793
9. NeuAirth 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
10. Zhou HX Shan Y: Prediction of protein interaction sites from sequence profile and residue neighbour list. Proteins 2001, 44:336-343. 10.1002/ prot.1099 11455607
11. Chakrabarti P Janin J: Dissecting protein-protein recognition sites. Proteins 2002, 47:334-343. 11948787 10.1002/prot.10085
12. Jones S Thornton JM: Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996, 93:13-20. 40170 8552589 10.1073/pnas.93.1.13
13. Tsai CJ Lin SL Wolfson HJ Nussinov R: Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect. Protein Sci 1997, 6:53-64. 2143524 9007976
14. Jones S Thornton JM: Analysis of protein-protein interaction sites using surface patches. J Mol Biol 1997, 272:121-132. 10.1006/jmbi.1997.1234 9299342
15. TPong H Qin S Zhou HX: PI2PE: protein interface/interior prediction engine. Nucleic Acid Res 2007, 35:W357-W362. 1933225 17526530 10.1093/ nar/gkm231
16. Hu Z Ma B Wolfson H Nussinov R: Conservation of polar residue as hot spots at protein interfaces. Proteins 2000, 39:331-342. 10.1002/ (SICI)1097-0134(20000601)39:4<331::AID-PROT60>3.0.CO;2-A 10813815
17. Ma B Elkayam T Wolfson H Nussinov: Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci USA 2003, 100:5772-5777. 156276 12730379 10.1073/pnas.1030237100
18. Jones S Thornton JM: ProAein-protein interactions: a review of protein dimer structures Prog Biophys. Mol Biol 1995, 63:31-65. 10.1016/ 0079-6107(94)00008-W 7746868
19. Chen H Zhou HX: Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data. Proteins 2005, 61:21-35. 10.1002/prot.20514 16080151
20. Liang S Zhang C Liu S Zhou Y: Protein binding site prediction using an empirical scoring function. Nucleic Acids Res 2006, 34:3698-3707. 1540721 16893954 10.1093/nar/gkl454
21. Lichtarge O Bourne HR Cohen FE: An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996, 257:342-358. 10.1006/jmbi.1996.0167 8609628
22. Lichtarge O Sowa ME: Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol 2002, 12:21-27. 10.1016/ S0959-440X(02)00284-1 11839485
23. Madabushi S Yao H Marsh M Kristensen DM Philippi A Sowa ME Lichtarge O: Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J Mol Biol 2002, 316:139-154. 10.1006/jmbi.2001.5327 11829509
24. Yao H Kristensen DM Mihalek I Sowa ME Shaw C Kimmel M Kavraki L Lichtarge O: An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol 2003, 326:255-261. 10.1016/S0022-2836(02)01336-0 12547207
25. Yao H MihaleA I Lichtarge O: Rank information: a structure-independent measure of evolutionary trace quality that improves identification of protein functional sites. Proteins 2006, 65:111-123. 10.1002/prot.21101 16894615
26. Aloy P Querol E Aviles FX Sternberg MJE: Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 2001, 311:395-408. 10.1006/ jmbi.2001.4870 11478868
27. de Vries SJ van Dijk ADJ Bonvin AMJJ: WHISKY: What information does surface conservation yield? Application to data-driven docking. Proteins 2006, 63:479-489. 10.1002/prot.20842 16450362
28. Chung; JL Wang W Bourne PE: Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins 2006, 62:630-640. 10.1002/prot.20741 16329107
29. Bradford JR Needham CJ Bulpitt AJ Westhead DR; Insights into protein-protein interfaces using a Bayesian network prediction method. J Mol Biol 2006, 362:365-386. 10.1016/j.jmb.2006.07.028 16919296
30. Bradford JR Westhead DR: Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005, 21:1487-1494. 10.1093/bioinformatics/bti242 15613384
31. Fariselli P Pazos F Valencia A Casadio R: Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 2002, 269:1356-1361. 10.1046/j.1432-1033.2002.02767.x 11874449
32. Yan C Dobbs D Honavar D: A two-staged classifier for identification of protein-protein interface residues. Bioinformatics 2004, 20:i371-i378. 10.1093/bioinformatics/bth920 15262822
33. Koike A Takagi T; Prediction of protein-protein interaction sites using support vector machines. Protein Eng Des Sel 2004, 17:165-173. 10.1093/ protein/gzh020 15047913
34. Block P Paern J Hullermeier E Sanschagrin P Sotriffer CA Klebe G: Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms. Proteins 2006, 65:607-622. 10.1002/prot.21104 16955490
35. Armon A Graur D Ben-Tal N: ConSurf: An algorithm tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 2001, 307:447-463. 10.1006/ jmbi.2000.4474 11243830
36. del Sol Mesa A Pazos F Valencia A: Automatic methods for predicting functionally important residues. J Mol Biol 2003, 326:1289-1302. 10.1016/ S0022-2836(02)01451-1 12589769
37. Darnell SJ Page D Mitchell JC: An automated decision-tree approach to predicting protein interaction hot spots. Proteins 2007, 68:813-823. 10.1002/prot.21474 17554779
38. Pufareva I Budagyan L Raush E Totrov M Abagyan R: PIER: protein interface recognition for structural proteomics. Proteins 2007, 67:400-417. 10.1002/prot.21233 17299750
39. 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. 102472 10592235 10.1093/nar/28.1.235
40. Mintseris J Wiehe K Pierce B Anderson R Chen R Janin J Weng Z: Protein-Protein Docking Benchmark 2.0: An update. Proteins 2005, 60:214-216. 10.1002/prot.20560 15981264
41. Zhang C Vasmatzis G Cornette JL DeLisi C: Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997, 267:707-726. 10.1006/jmbi.1996.0859 9126848
42. Li N Sun Z Jiang F: SOFTDOCK application to protein-protein interaction benchmark and CAPRI. Proteins 2007, 69:801-808. 10.1002/prot.21728 17803216
43. Sweet RM Eisenberg D: Correlation of sequence hydrophobicities measures similarity in three dimensional protein structure. J Mol Biol 1983, 171:479-488. 10.1016/0022-2836(83)90041-4 6663622
44. Kabsch W Sandor C: Dictionary of protPin secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637. 10.1002/bip.360221211 6667333
45. Rost B Sander C: Conservation and prediction of solvent accessibility in protein families. Proteins 1994, 20:216-226. 10.1002/prot.340200303 7892171
46. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ: Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 146917 9254694 10.1093/ nar/25.17.3389
47. The UniProt Consortium: The Universal Protein Resource (Uniprot) Nucleic Acids Res 2008, 36:D190-D195. 2238893 18045787 10.1093/nar/gkm895
48. Bowie JU Luthy R Eisenberg D: A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253:164-170. 10.1126/science.1853201 1853201
49. Fan R Chen P Lin C: Working set selection using the second order information for training. SVM J Mach Learn Res 2005, 6:1889-1918.
50. Press WH Teukolsky SA Vetterling WT Flannery BP: Numerical Recipes in C Cambridge: Cambridge University Press 2 1995
51. R Development Core Team R: A Language and Environment for Statistical Computing. Austria 2008