Improved prediction of protein-protein binding sites using a support vector machines approach

Bioinformatics

Volumn 21, Issue 8, 2005, Pages 1487-1494

  Bradford, James R ^a   Westhead, David R ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; BIOINFORMATICS; CALCULATION; COMPUTER PROGRAM; CONTROLLED STUDY; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DATA BANK; PROTEIN STRUCTURE; PROTEOMICS; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY; STRUCTURAL GENOMICS; VALIDATION PROCESS;

EID: 17444372787     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti242     Document Type: Article

References (61)

1. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
3. Bradford,J.R. and Westhead,D.R. (2003) Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem. Protein Sci., 12, 2099-2103.
4. Brown,M., Grundy,W., Lin,D., Cristianini,N., Sugnet,C., Ares,M. and Haussler,D. (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci., 97, 262-267.
5. Caffrey,D.R., Somaroo,S., Hughes,J.D., Mintseris,J. and Huang,E.S. (2004) Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci., 13 190-202.
6. Chothia,C. and Janin,J. (1975) Principles of protein-protein recognition. Nature, 256, 705-708.
7. Connolly,M.L. (1983) Analytical molecular surface calculation. J. Appl. Crystallogr., 16, 548-558.
8. Cristianini,N. and Shawe-Taylor,J. (2000) Support Vector Machines and Other Kernel-based learning Methods. Cambridge University Press, Cambridge, MA.
9. Ding,C.H. and Dunchak,I. (2001) Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics, 17, 349-358.
10. Dobson,P.D. and Doig,A.J. (2003) Distinguishing enzyme structures from non-enzymes without alignments. J. Mol. Biol., 330, 771-783.
11. Duncan,B.S. and Olson,A.J. (1993) Shape analysis of molecular surfaces. Biopolymers, 33, 231-238.
12. Fariselli,P., Pazos,F., Valencia,A. and Casadio,R. (2002) Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur. J. Biochem., 269, 1356-1361.
13. Fauchère,J.L. and Pliska,V. (1983) Hydrophobic parameters of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem., 18, 369-375.
14. Glaser,F., Steinberg,D.M., Vakser,I.A. and Ben-Tal,N. (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins, 43, 89-102.
15. Griffith,J.P., Kim,J.L., Kim,E.E., Sintchak,M.D., Thomson,J.A., Fitzgibbon,M.J., Fleming,M.A., Caron,P.R., Hsiao,K. and Navia,M.A. (1995) X-ray structure of calcineurin inhibited by the Immunophilin-immunosuppressant FKBP12-FK506 complex. Cell, 82 507-522.
16. Halperin,I., Ma,B., Wolfson,H. and Nussinov,R. (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins, 47, 409-443.
17. Hua,S. and Sun,Z. (2001) A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach. J. Mol. Biol., 308, 397-407.
18. Huse,M., Chen,Y.G., Massague,J. and Kuriyan,J. (1999) Crystal structure of the cytoplasmic domain of the type I TGF β-receptor in complex with FKBP12. Cell, 96, 425-436.
19. Joachims,T. (1999) Making large-scale SVM learning practical. In Advances in Kernel Methods - Support Vector Learning. The MIT Press, Cambridge, CA.
20. Jones,S. and Thornton,J.M. (1996) Principles of protein-protein Interactions. Proc. Natl Acad. Sci. USA, 93, 13-20.
21. Jones,S. and Thornton,J.M. (1997a) Analysis of protein-protein interaction sites using surface patches. J. Mol. Biol. 272, 121-132.
22. Jones,S. and Thornton,J.M. (1997b) Prediction of protein-protein interaction sites using patch analysis, J. Mol. Biol. 272, 133-143.
23. Keil,M., Exner,T.E. and Brickmann,J. (2004) Pattern recognition strategies for molecular surfaces: III. binding site prediction with a neural network. J. Comput. Chem., 25, 779-789.
24. Keskin,O., Tsai,C-J., Wolfson,H. and Nussinov,R. (2004) A new, structurally non-redundant, diverse data set of protein-protein interfaces and its implications. Protein Sci., 13, 1043-1055.
25. Kim,H. and Park,H. (2003) Protein secondary structure prediction based on an improved support vector machines approach. Protein Eng., 16, 553-560.
26. Koenderink,J.J. (1991) Solid Shape. The MIT Press, Cambridge, MA.
27. Koike,A. and Takagi,T. (2004) Prediction of protein-protein interaction sites using support vector machines. Protein Eng. Des. Sel., 17, 165-173.
28. Krishnan,V.G. and Westhead,D.R. (2003) A comparative study of machine learning methods to predict the effects of Single Nucleotide Polymorphisms on protein function. Bioinformatics, 19, 2199-2209.
29. Larsen,T.A., Olson,A.J. and Goodsell,D.S. (1998) Morphology of protein-protein interfaces. Structure, 6, 421-427.
30. Livingstone,C.D. and Barton,G.J. (1993) Protein sequence alignments - a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci., 9, 745-756.
31. Lo Conte,L., Chothia,C. and Janin,J. (1999) The atomic structure of Protein-protein recognition sites. J. Mol. Biol., 285, 2177-2198.
32. Neuvirth,H., Raz,R. and Schreiber,G. (2004) ProMate: A structure based prediction program to identify the location of protein-protein binding sites. J. Mol. Biol., 338, 181-199.
33. Nooren,I.M. and Thornton,J.M. (2003a) Diversity of protein-protein Interactions. EMBO J., 22, 3486-3492.
34. Nooren,I.M. and Thornton,J.M. (2003b) Structural characterisation and functional significance of transient protein-protein interactions. J. Mol. Biol., 325, 991-1018.
35. Preissner,R., Goede,A. and Frommel,C. (1998) Dictionary of interfaces in proteins (DIP). Data bank of complementary molecular surface patches. J. Mol. Biol., 280, 535-550.
36. Raman,C.S., Li,H., Martasek,P., Kral,V., Masters,B.S. and Poulos,T.L. (1998) Crystal structure of constitutive endothelial nitric oxide synthase: a paradigm for pterin function involving a novel metal center. Cell, 95, 939-950.
37. Rao,V.D., Misra,S., Boronenkov,I.V., Anderson,R.A. and Hurley,J.H. (1998) Structure of type II β-phosphatidylinositol phosphate kinase: a protein kinase fold flattened for interfacial phosphorylation. Cell, 94, 829-839.
38. Rittinger,K., Walker,P.A., Eccleston,J.F., Smerdon,S.J. and Gamblin,S.J. (1997) Structure at 1.65 Å of RhoA and its GTPase-activating protein in complex with a transition-state analogue. Nature, 389, 758-762.
39. Rocchia,W., Alexov,E. and Honig,B. (2001) Extending the applicability of the non-linear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions. J. Phys. Chem. B., 105, 6507-6514.
40. Rocchia,W., Sridharan,S., Nicholls,A., Alexov,E., Chiabrera,A. and Honig,B. (2002) Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method. J. Comp. Chem., 23, 128-137.
41. Rüping,S. (2000) MySVM. University of Dortmund, Dortmund, Germany.
42. Sanner,M.F. and Olson,A.J. (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38, 305-320.
43. Siepen,J.A., Radford,S.E. and Westhead,D.R. (2003) β edge strands in protein structure prediction and aggregation. Protein Sci. 12, 2348-2359.
44. Tabernero,L., Bochar,D.A., Rodwell,V.W. and Stauffacher,C.V. (1999) Substrate-induced closure of the Flap domain in the ternary complex structures provides insights into the mechanism of catalysis by 3-hydroxy-3-methylglutaryl-CoA reductase. Proc. Natl Acad. Sci. USA 96, 7167-7171.
45. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
46. Tsai,C-J., Lin,S.L., Wolfson,H.J. and Nussinov,R. (1996) A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J. Mol. Biol., 260, 604-620.
47. Valdar,W.S. (2002) Scoring residue conservation. Proteins 48, 227-241.
48. Vapnik,V.N. (1998) Statistical Learning Theory. J. Wiley and sons, New York.
49. Wei,Y., Contreras,J.A., Sheffield,P., Osterlund,T., Derewenda,U., Kneusel,R.E., Matern,U., Holm,C. and Derewenda,Z.S. (1999) Crystal structure of brefeldin A esterase, a bacterial homolog of the mammalian hormone-sensitive lipase. Nat. Struct. Biol., 6, 340-345.
50. Weiner,S.J., Kollman,P.A., Case,D.A., Singh,U.C., Ghio,C., Alagona,G., Profeta,S.Jr. and Weiner,P. (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc., 106, 765-784.
51. Williams,P.A., Fulop,V., Garman,E.F., Saunders,N.F., Ferguson,S.J. and Hajdu,J. (1997) Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme. Nature, 389, 406-412.
52. Yan,C., Dobbs,D. and Honavar,V. (2003) Identification of residues involved in protein-protein interaction from amino acid sequence - a support vector machine approach. In Abraham,A., Franke,K. and Köppen,M. (eds), Intelligent Systems Design and Applications. Springer-Verlag, Berlin, Germany, pp. 53-62.
53. Yan,C., Dobbs,D. and Honavar,V. (2004) A two stage classifier for identification of protein-protein interface residues. Bioinformatics, 20, i371-i378.
54. Young,L., Jernigan,R.L. and Covell,D.G. (1994) A role for surface hydrophobicity in protein-protein recognition. Protein Sci. 3, 717-729.
55. Yuan,Z., Burrage,K. and Mattick,J.S. (2002) Prediction of protein solvent accessibility using support vector machines. Proteins 48, 566-570.
56. Zachmann,C-D., Heiden,W., Schlenkrich,M. and Brickmann,J. (1992) Topological analysis of complex molecular surfaces. J. Comp. Chem., 13, 76-84.
57. Zavaljevski,N., Stevens,F.J. and Reifman,J. (2002) Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions. Bioinformatics, 18, 689-696.
58. Zhang,S-W., Quan,P., Zhang,H-C., Zhang,Y-L. and Wang,H-Y. (2003) Classification of protein quaternary structure with support vector machine. Bioinformatics, 19, 2390-2396.
59. Zhao,Y., Clemencia,P., Valmori,D., Martin,R. and Simon,R. (2003) Application of support vector machines for T-cell epitopes prediction. Bioinformatics, 19, 1978-1984.
60. Zhou,H.X. and Shan,Y. (2001) Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins, 44, 336-343.
61. Zvelebil,M.J., Barton,G.J., Taylor,W.R. and Sternberg,M.J. (1987) Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J. Mol. Biol., 195, 957-961.