Efficient design of bio-basis function to predict protein functional sites using kernel-based classifiers

IEEE Transactions on Nanobioscience

Volumn 9, Issue 4, 2010, Pages 242-249

  Maji, Pradipta ^a   Das, Chandra ^b  

^a INDIAN STATISTICAL INSTITUTE   (India)

^b NETAJI SUBHASH ENGINEERING COLLEGE   (India)

Author keywords

Bioinformatics; functional site prediction; pattern recognition; sequence analysis; support vector machines

Indexed keywords

BASIS FUNCTIONS; EFFICIENT DESIGNS; EFFICIENT METHOD; FISHER RATIO; FUNCTIONAL SITES; KERNEL BASED CLASSIFIERS; KERNEL FUNCTION; NOVEL CONCEPT; NUMERICAL FEATURES; PATTERN RECOGNITION ALGORITHMS; PROTEIN FUNCTIONAL SITES; SEQUENCE ANALYSIS; SEQUENCE SPACE; STRING KERNEL; SUPPORT VECTOR; ZONE OF INFLUENCES;

AMINO ACIDS; BIOINFORMATICS; INTEGRATION; PATTERN RECOGNITION; SUPPORT VECTOR MACHINES;

FORECASTING;

ALGORITHM; ARTICLE; ARTIFICIAL NEURAL NETWORK; AUTOMATED PATTERN RECOGNITION; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; INFORMATION RETRIEVAL; METHODOLOGY; PROTEIN BINDING; SEQUENCE ANALYSIS;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; INFORMATION STORAGE AND RETRIEVAL; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); PATTERN RECOGNITION, AUTOMATED; PROTEIN BINDING; SEQUENCE ANALYSIS, PROTEIN;

EID: 79251553484     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2010.2080684     Document Type: Article

References (35)

1. P. Arrigo, F. Giuliano, and G. Damiani, "Identification of a new motif on nucleic acid sequence data using Kohonen's self-organising map," CABIOS, vol. 7, pp. 353-357, 1991.
2. E. A. Ferran and P. Ferrara, "Topological maps of protein sequences," Biol. Cybern., vol. 65, pp. 451-458, 1991.
3. Y. D. Cai and K. C. Chou, "Artificial neural network model for predicting HIV protease cleavage sites in protein," Adv. Eng. Softw., vol. 29, no. 2, pp. 119-128, 1998.
4. P. Baldi, G. Pollastri, C. A. Anderson, and S. Brunak, "Matching protein beta-sheet partners by feedforward and recurrent neural networks," in Proc. Int. Conf. Intell. Syst. Mol. Biol. (ISMB), 1995, vol. 8, pp. 25-36.
5. P. Baldi and S. Brunak, Bioinformatics: The Machine Learning Approach. Cambridge, MA: MIT Press, 1998.
6. Z. R. Yang, "Biological application of support vector machines," Briefings Bioinf., vol. 5, no. 4, pp. 328-338, 2004.
7. S. F. Altschul, W. Gish, W. Miller, E.Myers, and D. J. Lipman, "Basic local alignment search tool," J. Mol. Biol., vol. 215, pp. 403-410, 1990.
8. A. V. Aho and M. Corasick, "Efficient string matching: An aid to bibliographic search," Commun. ACM, vol. 18, no. 6, pp. 333-340, 1975.
9. K. Thompson, "Regular expression search algorithm," Commun. ACM, vol. 11, no. 6, pp. 419-422, 1968.
10. D. B. Searls and K. P. Murphy, "Automata-theoretic models of mutation and alignment," in Proc. 3rd Int. Conf. Intell. Syst. Mol. Biol., 1995, pp. 341-349.
11. D. B. Searls, "Sequence alignment through pictures," Trends Genet., vol. 12, pp. 35-37, 1996.
12. N. Qian and T. J. Sejnowski, "Predicting the secondary structure of globular proteins using neural network models," J. Mol. Biol., vol. 202, pp. 865-884, 1988.
13. A. Narayanan, X. K.Wu, and Z. R.Yang, "Mining viral protease data to extract cleavage knowledge," Bioinformatics, vol. 18, pp. 5-13, 2002.
14. R. Thomson, C. Hodgman, Z. R. Yang, and A. K. Doyle, "Characterising proteolytic cleavage site activity using bio-basis function neural network," Bioinformatics, vol. 19, no. 14, pp. 1741-1747, 2003.
15. E. A. Berry, A. R. Dalby, and Z. R. Yang, "Reduced bio-basis function neural network for identification of protein phosphorylation sites: Comparison with pattern recognition algorithms," Comput. Biol. Chem., vol. 28, pp. 75-85, 2004.
16. Z. R. Yang and R. Thomson, "Bio-basis function neural network for prediction of protease cleavage sites in proteins," IEEE Trans. Neural Netw., vol. 16, no. 1, pp. 263-274, 2005.
17. Z. R. Yang, "Prediction of caspase cleavage sites using Bayesian biobasis function neural networks," Bioinformatics, vol. 21, no. 9, pp. 1831-1837, 2005.
18. Z. R. Yang, R. Thomson, P. McNeil, and R. Esnouf, "RONN: Use of the bio-basis function neural network technique for the detection of natively disordered regions in proteins," Bioinformatics, vol. 21, no. 16, pp. 3369-3376, 2005.
19. Z. R. Yang and K. C. Chou, "Predicting the linkage sites in glycoproteins using bio-basis function neural networks," Bioinformatics, vol. 20, no. 6, pp. 903-908, 2004.
20. Y. D. Cai, X. J. Liu, X. B. Xu, and K. C. Chou, "Support vector machines for predicting the specificity of GalNAc-transferase," Peptides, vol. 23, pp. 205-208, 2002.
21. Y. Minakuchi, K. Satou, and A. Konagaya, "Prediction of protein-protein interaction sites using support vector machines," Genome Inf., vol. 13, pp. 322-323, 2002.
22. A. Gutteridge, G. J. Bartlett, and J. M. Thornton, "Using a neural network and spatial clustering to predict the location of active sites in enzymes," J. Mol. Biol., vol. 330, pp. 719-734, 2003.
23. Y. Bengio and Y. Pouliot, "Efficient recognition of immunological domains from amino acid sequences using a neural network," CABIOS, vol. 6, pp. 319-324, 1990.
24. S. F. Altschul, M. S. Boguski, W. Gish, and J. C. Wootton, "Issues in searching molecular sequence databases," Nature Genet., vol. 6, pp. 119-129, 1994.
25. S. Henikoff and J. G. Henikoff, "Amino acid substitution matrices from protein blocks," PNSA, vol. 89, pp. 10 915-10 919, 1992.
26. M. S. Johnson and J. P. Overington, "A structural basis for sequence comparisons: An evaluation of scoring methodologies," J. Mol. Biol., vol. 233, pp. 716-738, 1993.
27. M. O. Dayhoff, R. M. Schwartz, and B. C. Orcutt, "A model of evolutionary change in proteins. Matrices for detecting distant relationships," in Atlas of Protein Sequence and Structure. Washington, DC: Nat. Biomed. Res. Found., 1978, vol. 5, pp. 345-358.
28. C. Shannon and W. Weaver, The Mathematical Theory of Communication. Urbana, IL: Univ. Illinois Press, 1964.
29. Z. R.Yang, "Orthogonal kernel machine for the prediction of functional sites in proteins," IEEE Trans. Syst., Man, Cybern. B, Cybern., vol. 35, no. 1, pp. 100-106, 2005.
30. R. O. Duda, P. E. Hart, and D. G. Stork, Pattern Classification. New York: Wiley, 2001.
31. A. Stojmirovic, "Quasi-metric spaces with measure," Topol. Proc., vol. 28, no. 2, pp. 655-671, 2004.
32. M. Itoh, S. Goto, T. Akutsu, and M. Kanehisa, "Fast and accurate database homology search using upper bounds of local alignment scores," Bioinformatics, vol. 21, no. 7, pp. 912-921, 2005.
33. Y. M. Lui and H.-D. Cheng, "A new peak selection criterion based on minimizing the classification error," Inf. Sci., vol. 94, pp. 213-233, 1996.
34. P. Maji, M. K. Kundu, and B. Chanda, "Second order fuzzy measure and weighted co-occurrence matrix for segmentation of brain MR images," Fundamenta Informaticae, vol. 88, no. 1-2, pp. 161-176, 2008.
35. P. Maji and C. Das, "Protein functional sites prediction using modified bio-basis function and quantitative indices," IEEE Trans. NanoBiosci., accepted for publication.