Inferring protein-protein interacting sites using residue conservation and evolutionary information

Protein and Peptide Letters

Volumn 13, Issue 10, 2006, Pages 999-1005

  Wang, Bing ^a,b   Wong, Hau San ^c   Huang, De Shuang ^a  

^a INSTITUTE OF INTELLIGENT MACHINES   (China)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^c CITY UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Conservation and evolution information; Protein protein interacting sites; Spatial neighboring residue; Support vector machines

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; ENTROPY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PREDICTION AND FORECASTING; PROTEIN ANALYSIS; SENSITIVITY AND SPECIFICITY; SURFACE PROPERTY; VALIDATION STUDY;

AMINO ACID SEQUENCE; CONSERVED SEQUENCE; ENTROPY; EVOLUTION, MOLECULAR; PREDICTIVE VALUE OF TESTS; PROTEIN INTERACTION MAPPING; PROTEINS; SENSITIVITY AND SPECIFICITY; SURFACE PROPERTIES;

EID: 33750619846     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986606778777498     Document Type: Article

References (29)

1. Alberts, B. (2002), Molecular Biology of the Cell. 4nd end. Garland Science, New York.
2. Kini, R.M. and Evans, H.J. (1996) FEBS Lett. 385, 81-6.
3. Valdar, W.S. and Thornton, J.M. (2001) J. Mol. Biol. 313, 399-416.
4. Sheinerman, F.B. and Honig, B. (2002) J. Mol. Biol. 318, 161-77.
5. Janin, J. (1997) Nat. Struct. Biol. 4, 973-4.
6. Thorn, K.S. and Bogan, A.A. (2001) Bioinformatics 17, 284-5.
7. Pazos, F. and Valencia, A. (2002) Proteins 47, 219-27.
8. Gallet, X., Charloteaux, B., Thomas, A. and Brasseur, R. (2000) J. Mol. Biol. 302, 917-26.
9. Jones, S. and Thornton, J.M. (1997) J. Mol. Biol. 272, 121-32.
10. Jones, S. and Thornton, J.M. (1997) J. Mol. Biol. 272, 133-43.
11. Kamp, R.M., Calvete, J.J. and Choli-Papadopoulou, T. (2004) Methods in proteome and protein analysis: Principles and practice., pp. xxxii, 404 Springer-Verlag, Berlin ; New York.
12. Zhou, H.X. and Shan, Y. (2001) Proteins 44, 336-43.
13. Ofran, Y. and Rost, B. (2003) FEBS Lett. 544, 236-9.
14. Fariselli, P., Pazos, F., Valencia, A. and Casadio, R. (2002) Eur. J. Biochem. 269, 1356-61.
15. Yan, C., Dobbs, D. and Honavar, V. (2004) Bioinformatics 20 Suppl 1, I371-I378.
16. Res, I., Mihalek, I. and Lichtarge, O. (2005) Bioinformatics 21, 2496-501.
17. Koike, A. and Takagi, T. (2004) Protein Eng. Des. Sel. 17, 165-73.
18. Lo Conte, L., Chothia, C. and Janin, J. (1999) J. Mol. Biol. 285, 2177-98.
19. Rost, B. and Sander, C. (1994) Proteins 20, 216-26.
20. Kabsch, W. and Sander, C. (1983) Biopolymers 22, 2577-637.
21. Dodge, C., Schneider, R. and Sander, C. (1998) Nucleic Acids Res. 26, 313-5.
22. Shannon, C.E. (1997) MD Comput. 14, 306-17.
23. Mirny, L.A. and Shakhnovich, E.I. (1999) J Mol. Biol. 291, 177-96.
24. Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T. and Ben-Tal, N. (2005) Nucleic Acids Res. 33, W299-302.
25. Glaser, F., Rosenberg, Y., Kessel, A., Pupko, T. and Ben-Tal, N. (2005) Proteins 58, 610-7.
26. Pupko, T., Bell, R.E., Mayrose, I., Glaser, F. and Ben-Tal, N. (2002) Bioinformatics 18 Suppl. 1, S71-7.
27. Duda, R.O., Hart, P.E. and Stork, D.G. (2001) Pattern classification. Wiley, New York.
28. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) Nucleic Acids Res. 28, 235-42.
29. Volbeda, A., Charon, M.H., Piras, C., Hatchikian, E.C., Frey, M. and Fontecilla-Camps, J.C. (1995) Nature 373, 580-7.