PECB: Prediction of enzyme catalytic residues based on Naïve Bayes classification

International Journal of Bioinformatics Research and Applications

Volumn 4, Issue 3, 2008, Pages 295-305

  Zhang, Kunpeng ^a   Xu, Yun ^a,b   Chen, Guoliang ^a,b  

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

^b Laboratory of High Performance Computing and Its Application   (China)

Author keywords

Bioinformatics; Catalytic residues; Enzyme; Na ve Bayes; PECB; Physico chemical; Sequence; Structure information

Indexed keywords

ACCURACY; ARTICLE; BAYES THEOREM; CATALYSIS; CLASSIFICATION ALGORITHM; ENZYME STRUCTURE; PHYSICAL CHEMISTRY; PROTEIN FUNCTION; PROTEIN STRUCTURE; RESIDUE ANALYSIS; SENSITIVITY AND SPECIFICITY;

EID: 47749106409     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2008.019576     Document Type: Article

References (25)

1. Alexandra, S.P., Ruth, N. and J, W.H. (2004) 'Recognition of functional sites in protein structures', J. Mol. Biol., Vol. 339, No. 3, pp.607-633.
2. 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., Vol. 25, No. 17, pp.3389-3402.
3. 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., Vol. 28, pp.235-242.
4. Bernstein. F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F.J., Brice, M.D., Rogers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1997) 'The Protein Data Bank: a computer-based archival file for macromolecular structures', J. Mol. Biol., Vol. 330, No. 4, pp.719-734.
5. Buntine, W. (1991) 'Theory refinement on Bayesian networks', Proceedings of Seventh Conference on Uncertainty in Artificial Intelligence, Los Angeles, CA, pp.52-60.
6. David, H. (1996) A Tutorial on Learning with Bayesian Networks, Microsoft Research Technical Report, revised edition, Edited by Division AT, Redmond, WA, 98052, One Microsoft Way.
7. Elcock, A. (2001) 'Prediction of functionally important residues based solely on the computed energetics of protein structure', J. Mol. Biol., Vol. 312, pp.885-896.
8. Ferr, F., Ausiello, G., Zanzoni, A. and Helmer-Citterich, M. (2004) 'SURFACE: a database of protein surface regions for functional annotation', Nucleic Acids Res., Vol. 32, pp.240-244.
9. Gutteridge, A., Bartlett, G. and Thornton, J. (2003) 'Using a neural network and spatial clustering to predict the location of active sites in enzymes', J. Mol. Biol., Vol. 330, No. 4, pp.719-734.
10. Hegyi, H. and Gerstein, M. (1999) 'The relationship between protein structure and function: a comprehensive survey with application to the yeast genome', J. Mol. Biol., Vol. 288, pp.147-164.
11. Higgins, D.J., Thompson, T., Gibson, J.D., Thompson, D.G., Higgins and Gibson, T.J. (1994) 'CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice', Nucleic Acids Res., Vol. 22, pp.4673-4680.
12. Hubbard, S.J. and Thornton, J.M. (2003) 'NACCESS: Computer Program, Department of Biochemistry and Molecular Biology, University College, London', J. Mol. Biol.
13. Jiawei, H. and Micheline, K. (2001) Data Mining: Concepts and Techniques, Microsoft Research Technical Report, 1st ed., Morgan Kaufmann, Beijing.
14. Kabsch, W. and Sander, C. (1983) 'Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features', Biopolymers, Vol. 22, pp.2577-2637.
15. Kunpeng, Z., Yun, X., Yifei, S. and Guoliang, C. (2006) 'Using a neural networking method to predict protein phosphorylation sites with specic kinase', Proceedings of International Symposium on Neural Networks 2006,Chengdu, LNCS, pp.682-689.
16. Laskowski, R. (1995) 'SURFNET: a program for visualizing molecular surfaces, cavities and intermolecular interactions', J. Mol. Graph., Vol. 13, pp.323-330.
17. Lichtarge, O., Bourne, H. and Cohen, F. (1996) 'An evolutionary trace method defines binding surfaces common to protein families', J. Mol. Biol., Vol. 257, No. 2, pp.342-358.
18. Motonori, O., Kinoshita, K. and Nishikawa, K. (2003) 'Prediction of catalytic residues in enzyme based on known tertiary structure, stability profile, and sequence conservation', J. Mol. Biol., Vol. 327, pp.1053-1064.
19. Nakai, S., Li-Chan, E.C. and Dou, J. (2005) 'Pattern similarity study of functional sites in protein sequences: lysozymes and cystatins', BMC Biochem., Vol. 6, No. 9.
20. SanM̃ateo, C. and Kaufmann, M. (2005) Weka 3: Data Mining Software in Java, http://www.cs.waikato.ac.nz/ml/weka/
21. Tsou, C.L. (1993) 'Conformational flexibility of enzyme active sites', Progress in Physiological Sciences, Vol. 282, pp.380, 381.
22. Valdar, W.S.J. (2002) 'Scoring residue conservation', Proteins: Structure, Function, and Genetics, Vol. 43, No. 2, pp.227-241.
23. Witten, I. and Frank, E. (2000) 'Practical machine learning tools and techniques with Java implements', Data Mining, Morgan Kaufmann, San Mateo, CA.
24. Zoubin, G. (2004) 'Tutorial on Bayesian methods for machine learning', The Twenty-First International Conference on Machine Learning, Banff, Alberta, Canada, Edited by ACM.
25. Zvelebil, M. and Sternberg, M. (1998) 'Analysis and prediction of the location of catalytic residues in enzymes', Protein Eng., No. 2, pp.127-138.