Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks

BMC Bioinformatics

Volumn 12, Issue SUPPL. 1, 2011, Pages

  Monji, Hiroyuki ^a   Koizumi, Satoshi ^a   Ozaki, Tomonobu ^b   Ohkawa, Takenao ^a  

^a KOBE UNIVERSITY   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EXPERIMENTAL METHODS; LARGE-SCALE DATASETS; PREDICTION ACCURACY; PROTEIN INTERACTION; PROTEIN STRUCTURES; PROTEIN-PROTEIN INTERACTION NETWORKS; STRUCTURAL SIMILARITY; YEAST TWO HYBRID; PREDICTION PROCESS;

BIOINFORMATICS; FORECASTING;

PROTEINS;

PROTEIN;

ALGORITHM; ARTICLE; BINDING SITE; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; BINDING SITES; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 79951542182     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S1-S39     Document Type: Article

References (29)

1. Sacan A, Ozturk O, Ferhatosmanoglu H, Wang Y. LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins. Bioinformatics 2007, 23:709-716. 10.1093/bioinformatics/btl685, 17237050.
2. 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.
3. Zhou HX, Shan Y. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 2001, 44:336-343. 10.1002/prot.1099, 11455607.
4. Fariselli P, Pazos F, Valencia A, Casadio R. Prediction of protein-protein interaction sites in heterocomplexes with neural networks. European Journal of Biochemistry 2002, 269(5):1356-1361. 10.1093/bioinformatics/btl685, 17237050.
5. Ofran Y, Rost B. Predicted protein-protein interaction sites from local sequence information. FEBS Letters 2003, 544:236-239. 10.1016/S0014-5793(03)00456-3, 12782323.
6. Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins 2007, 66:630-645. 10.1002/prot.21248, 17152079.
7. 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.
8. Koike A, Takagi T. Prediction of protein-protein interaction sites using support vector machines. Protein Eng Des Sel 2004, 17(2):165-173. 10.1093/protein/gzh020, 15047913.
9. Bordner AJ, Abagyan R. Statistical analysis and prediction of protein-protein interfaces. Proteins 2005, 60:353-366. 10.1002/prot.20433, 15906321.
10. Res I, Mihalek I, Lichtarge O. An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics 2005, 21:2496-2501. 10.1093/bioinformatics/bti340, 15728113.
11. Zhou HX, Qin SB. Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics 2007, 23:2203-2209. 10.1093/bioinformatics/btm323, 17586545.
12. Vazquez A, Flammini A, Maritan A, Vespignani A. Global protein function prediction in protein-protein interaction networks. Nature Biotechnology 2003, 21:697-700. 10.1038/nbt825, 12740586.
13. Letovsky S, Kasif S. Predicting protein function from protein-protein interaction data:a probabilistic approach. Bioinformatics 2003, 19(Suppl.1):i197-i204. 10.1093/bioinformatics/btg1026, 12855458.
14. Xenarios I, Salwinski L, Duan XJ, Higney P, M KS, Eisenberg D. DIP, the Database of Interacting Proteins:a research tool for studying cellular networks of protein interactions. Bioinformatics 2002, 30(1):303-305.
15. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW. BIND-The Biomolecular Interaction Network Database. Nucleic Acids Research 2001, 29(1):242-245. 10.1093/nar/29.1.242, 29820, 11125103.
16. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003, 13(10):2363-2371. 10.1101/gr.1680803, 403728, 14525934.
17. Salwinski L, Eisenberg D. Computational methods of analysis of protein-protein interactions. Current Opinion in Structural Biology 2003, 13:377-382. 10.1016/S0959-440X(03)00070-8, 12831890.
18. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM. A comprehensive analysis of proteinprotein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627. 10.1038/35001009, 10688190.
19. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A 2000, 97(3):1143-1147. 10.1073/pnas.97.3.1143, 15550, 10655498.
20. Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol 2000, 18:1257-1261. 10.1038/82360, 11101803.
21. Hishigaki H, Nakai K, Ono T, Tanagami A, Takagi T. Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 2001, 18(6):523-531. 10.1002/yea.706, 11284008.
22. Thomas A, Cannings R, Monk NAM, Cannings C. On the structure of protein-protein interaction networks. Biochemical Society Transactions 2003, 31:1491-1496. 10.1042/BST0311491, 14641097.
23. Deng M, Zhang K, Mehta S, Chen T, Sun F. Prediction of protein function using protein-protein interaction data. J Comput Biol 2002, 10(6):947-960.
24. Kinoshita K, Nakamura H. eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics 2004, 20:1329-1330. 10.1093/bioinformatics/bth073, 14871866.
25. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. CASTp, computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 2006, 34(Web Server issue):W116-W118. 10.1093/nar/gkl282, 1538779, 16844972.
26. Laskowski RA. SURFNET, a program for visualizing molecular surfaces, cavities, and intermolecular interactions. Journal of molecular graphics 1995, 13(5):323-330. 10.1016/0263-7855(95)00073-9, 8603061.
27. Huang B, Schroeder M. LIGSITE: predicting protein binding sites using the Connolly surface and degree of conservation. BMC structural Biology 2006, 6(19). 1601958, 16995956.
28. Kaneta Y, Shoji N, Ohkawa T, Nakamura H. A method of comparing protein molecular surface based on normal vectors with attributes and its application to function identification. Information Sciences 2002, 146(1-4):41-54.
29. Ritchie DW, Kemp GJL. Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. Jornal of Computational Chemistry 1999, 20(4):383-395.