A two-stage classifier for identification of protein-protein interface residues

Bioinformatics

Volumn 20, Issue SUPPL. 1, 2004, Pages

  Yan, Changhui ^a,b   Dobbs, Drena ^a   Honavar, Vasant ^a,b  

^a IOWA STATE UNIVERSITY   (United States)

^b Iowa State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; BAYES THEOREM; BINDING AFFINITY; BINDING SITE; CONFERENCE PAPER; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION;

EID: 13244292990     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth920     Document Type: Conference Paper

References (33)

1. Baldi, P., Brunak, S., Chauvin, Y. and Andersen, C.A.F. (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics, 16, 412-424.
2. Buntine, W. (1991) Theory refinement on Bayesian networks. Proceedings of Seventh Conference on Uncertainty in Artificial Intelligence. Morgan-Kaufmann, San Francisco, CA, USA. pp. 52-60.
3. Chakrabarti, P. and Janin, J. (2002) Dissecting protein-protein recognition sites. J. Mol. Biol., 272, 132-143.
4. Chothia, C. and Janin, J. (1975) Principles of protein-protein recognition. Nature, 256, 705-708.
5. Eisenberg, D., Schwarz, E., Komaromy, M. and Wall, R. (1984) Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol., 179, 125-142.
6. Fariselli, P., Pazos, F., Valencia, A. and Casadia, R. (2002) Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur. J. Biochem., 269, 1356-1361.
7. Gallet, X., Charloteaux, B., Thomas, A. and Brasseur, R. (2000) A fast method to predict protein interaction sites from sequences. J. Mol. Biol., 302, 917-926.
8. Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y.L., Ooi, C.E., Godwin, B., Vitols, E. et al. (2003) A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.
9. 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.
10. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S., Millar, A., Taylor, P., Bennett, K., Boutilier, K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
11. Jones, S. and Thornton, J.M. (1996) Principles of protein-protein interactions. Proc. Natl Acad. Sci., USA, 93, 13-20.
12. Jones, S. and Thornton, J.M. (1997) Prediction of protein-protein interaction sites using patch analysis. J. Mol. Biol., 272, 133-143.
13. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
14. Keskin, O., Bahar, I., Badretdinov, A.Y., Ptitsyn, O.B. and Jernigan, R.L. (1998) Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Sci. 7, 2578-2586.
15. Kini, R.M. and Evans, H.J. (1996) Prediction of potential protein-protein interaction sites from amino acid sequence identification of a fibrin polymerization site. FEBS Lett., 385, 81-86.
16. Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P., Han, J.J., Chesneau, A., Hao, T. et al. (2004) A map of the interactome network of the metazoan C. elegans. Science, 303, 540-543.
17. Lo Conte, L., Chothia, C. and Janin, J. (1999) The atomic structure of protein-protein recognition sites. J. Mol. Biol., 285, 2177-2198.
18. Lu, L., Arakaki, A.K., Lu, H. and Skolnick, J. (2003) Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome Res., 13, 1146-1154.
19. Mucchielli-Giorgi, M.H., About, S. and Puffery, P. (1999) PredAcc: prediction of solvent accessibility. Bioinformatics, 15, 176-177.
20. Naderi-Manesh, H., Sadeghi, M., Arab, S. and Movahedi, A.A.M. (2001) Prediction of protein surface accessibility with information theory. Proteins, 42, 452-459.
21. Ofran, Y. and Rost, B. (2003a) Analysing six types of protein-protein interfaces. J. Mol. Biol., 325, 377-387.
22. Ofran, Y. and Rost, B. (2003b) Predicted protein-protein interaction sites from local sequence information. FEBS Lett., 544, 236-239.
23. Pazos, F., Helmer-Citterich, M., Ausiello, G. and Valencia, A. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol., 271, 511-523.
24. Platt, J. (1998) Fast Training of Support Vector Machines using Sequential Minimal Optimization. MIT Press, Cambridge, MA.
25. Rost, B. and Sander, C. (1994) Conservation and prediction of solvent accessibility in protein families. Proteins, 20, 216-226.
26. Sheinerman, F.B. and Honig, B. (2002) On the role of electrostatic interactions in the design of protein-protein interfaces. J. Mol. Biol., 318, 161-177.
27. Teichmann, S.A., Murzin, A.G. and Chothia, C. (2001) Determination of protein function, evolution and interactions by structural genomics. Curr. Opin. Struct. Biol., 11, 354-363.
28. Valdar, W.S. and Thornton, J.M. (2001) Conservation helps to identify biologically relevant crystal contacts. J. Mol. Biol., 313, 399-416.
29. Valencia, A. and Pazos, F. (2002) Computational methods for prediction of protein interactions. Curr. Opin. Struct. Biol., 12, 368-373.
30. Valencia, A. and Pazos, F. (2003) Prediction of protein-protein interactions from evolutionary information. In Bourne, P.E. and Weissig, H. (eds), Structural Bioinformatics. Wiley Inc., pp. 411-426.
31. Witten, I.H. and Frank, E. (1999) Data Mining: Practical Machine Learning Tools and Techniques with Java Implements. Morgan Kaufmann, San Mateo, CA.
32. 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.
33. Zhou, H. and Shan, Y. (2001) Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins, 44, 336-343.