Large-scale prediction of protein-protein interactions from structures

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Hue, Martial ^a,b,c   Riffle, Michael ^d,e   Vert, Jean Philippe ^a,b,c   Noble, William S ^e,f  

^a PSL RESEARCH UNIVERSITY   (France)

^b INSTITUT CURIE   (France)

^c INSERM U900   (France)

^d UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF WASHINGTON   (United States)

^f University of Washington   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETTER PERFORMANCE; EXPERIMENTAL METHODS; LARGE-SCALE PREDICTION; MOLECULAR MECHANISM; PROTEIN INTERACTION; PROTEIN-PROTEIN INTERACTIONS; STATISTICAL PATTERN RECOGNITION; STRUCTURE INFORMATION;

FORECASTING; SUPPORT VECTOR MACHINES;

PROTEINS;

PROTEIN;

ARTICLE; BINDING SITE; CHEMISTRY; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEOMICS; SEQUENCE ANALYSIS;

BINDING SITES; DATABASES, PROTEIN; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN;

EID: 77952305592     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-144     Document Type: Article

References (31)

1. Deane CM, Salwinski L, Xenarios I, Eisenberg D. Two Methods for Assessment of the Reliability of High Throughput Observations. Molecular & Cellular Proteomics 2002, 1:349-356.
2. Russell BB, Aloy P. Targeting and tinkering with interaction networks. Nature Chemical Biology 2008, 4(11):666-673. 10.1038/nchembio.119, 18936751.
3. Grünberg R, Nilges M, Leckner J. Flexibility and Conformational Entropy in Protein-Protein Binding. Structure 2006, 14:683-693. 10.1016/j.str.2006.01.014, 16615910.
4. Kiel C, P Beltrao LS. Analyzing Protein Interaction Networks Using Structural Information. Annual Review of Biochemistry 2008, 77:415-441. 10.1146/annurev.biochem.77.062706.133317, 18304007.
5. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003, 302:449-453. 10.1126/science.1087361, 14564010.
6. Bock JR, Gough DA. Predicting protein-protein interactions from primary structure. Bioinformatics 2001, 17:455-460. 10.1093/bioinformatics/17.5.455, 11331240.
7. Dohkan S, Koike A, Takagi T. Improving the performance of an SVM-based method for predicting protein-protein interactions. In Silico Biology 2006, 6(6):515-529.
8. Gomez SM, Noble WS, Rzhetsky A. Learning to predict protein-protein interactions. Bioinformatics 2003, 19:1875-1881. 10.1093/bioinformatics/btg352, 14555619.
9. Ben-Hur A, Noble WS. Kernel methods for predicting protein-protein interactions. Bioinformatics 2005, 21(suppl 1):i38-i46. 10.1093/bioinformatics/bti1016, 15961482.
10. Chen X, Liu M. Prediction of protein-protein interactions using random decision forest framework. Bioinformatics 2005, 21(24):4394-4400. 10.1093/bioinformatics/bti721, 16234318.
11. Zhang LV, Wong S, King O, Roth F. Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 2004, 5:38-53. 10.1186/1471-2105-5-38, 419405, 15090078.
12. Qi Y, Klein-Seetharaman J, Bar-Joseph Z. Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources. Proceedings of the Pacific Symposium on Biocomputing 2005,
13. Shoemaker BA, Panchenko AR. Deciphering protein-protein interactions. Part 2. Computational methods to predict protein-protein interaction partners. Plos Computational Biology 2007, 3(4):595-601.
14. Qi Y, Bar-Joseph Z, Klein-Seetharaman J. Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins: Structure, Function, and Bioinformatics 2006, 63:490-500.
15. Qiu J, Hue M, Ben-Hur A, Vert JP, Noble WS. A structural alignment kernel for protein structures. Bioinformatics 2007, 23(9):1090-1098. 10.1093/bioinformatics/btl642, 17234638.
16. Vert JP, Qiu J, Noble WS. A new pairwise kernel for biological network inference with support vector machines. BMC Bioinformatics 2007, 8(Suppl 10):S8. 10.1186/1471-2105-8-S10-S8, 2230501, 18269702.
17. Schölkopf B, Smola A. Learning with Kernels 2002, Cambridge, MA: MIT Press.
18. Boser BE, Guyon IM, Vapnik VN. A Training Algorithm for Optimal Margin Classifiers. 5th Annual ACM Workshop on COLT 1992, 144-152. Pittsburgh, PA: ACM Press, Haussler D.
19. Noble WS. Support vector machine applications in computational biology. Kernel methods in computational biology 2004, 71-92. Cambridge, MA: MIT Press, Schoelkopf B, Tsuda K, Vert JP.
20. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering 1998, 11:739-747. 10.1093/protein/11.9.739, 9796821.
21. Holm L, Sander C. Protein Structure Comparison by Alignment of Distance Matrices. Journal of Molecular Biology 1993, 233:123-138. 10.1006/jmbi.1993.1489, 8377180.
22. Ortiz AR, Strauss CEM, Olmea O. MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison. Protein Science 2002, 11:2606-2621. 10.1110/ps.0215902, 2373724, 12381844.
23. Leslie C, Eskin E, Weston J, Noble WS. Mismatch String Kernels for SVM Protein Classification. Advances in Neural Information Processing Systems 2003, 1441-1448. Cambridge, MA: MIT Press, Becker S, Thrun S, Obermayer K.
24. Martin S, Roe D, Faulon JL. Predicting protein-protein interactions using signature products. Bioinformatics 2005, 21(2):218-226. 10.1093/bioinformatics/bth483, 15319262.
25. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP: the Database of Interacting Proteins. Nucleic Acids Research 2000, 28:289-291. 10.1093/nar/28.1.289, 102387, 10592249.
26. 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 Research 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
27. Ben-Hur A, Noble W. Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics 2006, 20(Suppl 1):S2.
28. Davis J, Goadrich M. The relationship between precision-recall and ROC curves. Proceedings of the International Conference on Machine Learning 2006,
29. Platt JC. Probabilities for support vector machines. Advances in Large Margin Classifiers 1999, 61-74. MIT Press, Smola A, Bartlett P, Schölkopf B, Schuurmans D.
30. Riffe M, Malmstrom L, Davis TN. The yeast resource center public data repository. Nucleic Acids Research 2005, 33:D378-D382. 10.1093/nar/gki073, 540027, 15608220.
31. Qiu J, Noble WS. Predicting co-complexed protein pairs from heterogeneous data. PLoS Computational Biology 2008, 4(4):e1000054. 10.1371/journal.pcbi.1000054, 2275314, 18421371.