Cport: A consensus interface predictor and its performance in prediction-driven docking with HADDOCK

PLoS ONE

Volumn 6, Issue 3, 2011, Pages

  de Vries, Sjoerd J ^a,b   Bonvin, Alexandre M J J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; ARTICLE; COMPLEX FORMATION; COMPUTER PROGRAM; INTERMETHOD COMPARISON; MOLECULAR DOCKING; PREDICTION; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SCORING SYSTEM; BIOLOGY; CHEMISTRY; METHODOLOGY; PROTEIN DATABASE; REPRODUCIBILITY;

MULTIPROTEIN COMPLEX;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MULTIPROTEIN COMPLEXES; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 79953040045     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0017695     Document Type: Article

References (40)

1. Stumpf MP, Thorne T, de Silva E, Stewart R, An HJ, et al. (2008) Estimating the size of the human interactome. Proc Natl Acad Sci U S A 105: 6959-6964.
2. Bonvin AM, (2006) Flexible protein-protein docking. Current Opinion in Structural Biology 16: 194-200.
3. Zhou HX, Qin S, (2007) Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics 23: 2203-2209.
4. de Vries SJ, Bonvin AM, (2008) How proteins get in touch: interface prediction in the study of biomolecular complexes. Curr Protein Pept Sci 9: 394-406.
5. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, et al. (2005) Protein-Protein Docking Benchmark 2.0: an update. Proteins 60: 214-216.
6. Dominguez C, Boelens R, Bonvin AMJJ, (2003) HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society 125: 1731-1737.
7. de Vries SJ, Melquiond ASJ, Kastritis PL, Karaca E, Bordogna A, et al. (2010) Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions. Proteins-Structure Function and Bioinformatics 78: 3242-3249.
8. de Vries SJ, van Dijk AD, Krzeminski M, van Dijk M, Thureau A, et al. (2007) HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69: 726-733.
9. van Dijk AD, Boelens R, Bonvin AM, (2005) Data-driven docking for the study of biomolecular complexes. Febs J 272: 293-312.
10. Melquiond ASJ, Bonvin AMJJ, (2010) Data-driven docking: using external information to spark the biomolecular rendez-vous. In: Zacharias M, editors. Protein-protein complexes: analysis, modelling and drug design pp. 183-209 Imperial College Press. London.
11. de Vries SJ, van Dijk ADJ, Bonvin AMJJ, (2006) WHISCY: What information does surface conservation yield? Application to data-driven docking. Proteins-Structure Function and Bioinformatics 63: 479-489.
12. Qin S, Zhou HX, (2007) meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformatics 23: 3386-3387.
13. Huang B, Schroeder M, (2008) Using protein binding site prediction to improve protein docking. Gene 422: 14-21.
14. Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R, (2007) PIER: protein interface recognition for structural proteomics. Proteins 67: 400-417.
15. Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES, (2004) Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 13: 190-202.
16. Ofran Y, Rost B, (2003) Analysing six types of protein-protein interfaces. J Mol Biol 325: 377-387.
17. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z, (2008) Protein-protein docking benchmark version 3.0. Proteins 73: 705-709.
18. Mendez R, Leplae R, De Maria L, Wodak SJ, (2003) Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 52: 51-67.
19. Fernandez-Recio J, Totrov M, Abagyan R, (2004) Identification of protein-protein interaction sites from docking energy landscapes. Journal of Molecular Biology 335: 843-865.
20. Hwang H, Vreven T, Pierce BG, Hung JH, Weng Z., Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins 78: 3104-3110.
21. Lensink MF, Wodak SJ, (2010) Blind predictions of protein interfaces by docking calculations in CAPRI. Proteins-Structure Function and Bioinformatics 78: 3085-3095.
22. Bradford JR, Westhead DR, (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 21: 1487-1494.
23. Martin O, Schomburg D, (2008) Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines. Proteins 70: 1367-1378.
24. Chen R, Li L, Weng Z, (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins 52: 80-87.
25. Wiehe K, Pierce B, Tong WW, Hwang H, Mintseris J, et al. (2007) The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins 69: 719-725.
26. Lensink MF, Mendez R, Wodak SJ, (2007) Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 69: 704-718.
27. Lensink MF, Wodak SJ, (2010) Docking and scoring protein interactions: CAPRI 2009. Proteins-Structure Function and Bioinformatics 78: 3073-3084.
28. Pierce B, Weng Z, (2007) ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 67: 1078-1086.
29. Pierce B, Weng Z, (2008) A combination of rescoring and refinement significantly improves protein docking performance. Proteins 72: 270-279.
30. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, et al. (1992) Molecular-Surface Recognition- Determination of Geometric Fit between Proteins and Their Ligands by Correlation Techniques. Proceedings of the National Academy of Sciences of the United States of America 89: 2195-2199.
31. Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, et al. (2003) Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins, Structure Function and Bioinformatics 52: 107-112.
32. Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, et al. (2007) Integrating statistical pair potentials into protein complex prediction. Proteins 69: 511-520.
33. Liang S, Meroueh SO, Wang G, Qiu C, Zhou Y, (2009) Consensus scoring for enriching near-native structures from protein-protein docking decoys. Proteins 75: 397-403.
34. de Vries SJ, van Dijk M, Bonvin AM, (2010) The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 5: 883-897.
35. Neuvirth H, Raz R, Schreiber G, (2004) ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 338: 181-199.
36. Chen H, Zhou HX, (2005) Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 61: 21-35.
37. Porollo A, Meller J, (2007) Prediction-based fingerprints of protein-protein interactions. Proteins 66: 630-645.
38. Liang S, Zhang C, Liu S, Zhou Y, (2006) Protein binding site prediction using an empirical scoring function. Nucleic Acids Res 34: 3698-3707.
39. Hubbard SJ, Thornton JM, (1993) NACCESS. University College London: Department of Biochemistry and Molecular biology. Available:http://www.bioinf.manchester.ac.uk/naccess.
40. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallographica Section D, Biological Crystallography 54 (Pt 5): 905-921.