A two-stage classifier for protein β-turn prediction using support vector machines

2006 IEEE International Conference on Granular Computing

Volumn , Issue , 2006, Pages 738-743

  Chiu, Hua Sheng ^a   Lin, Hsin Nan ^a   Lo, Allan ^a   Sung, Ting Yi ^a   Hsu, Wen Lian ^a  

^a INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

Author keywords

turn prediction; Classification; Protein secondary structure prediction; Support vector machines

Indexed keywords

APPROXIMATION THEORY; CORRELATION METHODS; DATABASE SYSTEMS; MOLECULAR STRUCTURE;

PREDICTION ACCURACY; PROTEIN SECONDARY STRUCTURE; SUPPORT VECTOR MACHINES (SVM);

PROTEINS;

EID: 33751113278     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (29)

1. J. S. Richardson, "The anatomy and taxonomy of protein structure," Adv. Protein Chem., vol. 34, pp. 167-339, 1981.
2. G. D. Rose, L. M. and J. A. Smith, "Turns in peptides and proteins", Adv. Protein Chem., vol. 37, pp. 100-109, 1985.
3. W. Kabsch and C. Sander, "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features," Biopolymers, vol. 22, pp. 2577-2637, 1983.
4. K. Takano, Y. Yamagata, and K. Yutani, "Role of amino acid residues at turns in the conformational stability and folding of human lysozyme," Biochemistry, vol. 39, pp. 8655-65, 2000.
5. K. C. Chou, "Prediction of tight turns and their types in proteins," Anal. Biochem., vol. 286, pp. 1-16, 2000.
6. P. N. Lewis, F. A. Momany and H. A. Scheraga, "Chain reversals in proteins," Biochem. Biophys. Acta., vol. 303, pp. 211-229, 1973.
7. P. Y. Chou and G. D. Fasman, "Conformational parameters for amino aicds in helical, β-sheet and random coil regions calculated from proteins," Biochemistry, vol. 13, pp. 211-222, 1974.
8. C. M. Wilmot and J. M. Thornton, "Analysis and prediction of the different types of β-turns in proteins," J. Mol. Biol., vol. 203, pp. 221-232, 1988.
9. E. G. Hutchinson and J. M. Thornton, "A revised set of potentials for beta-turn formation in proteins," Protein Sci, vol. 3, pp. 2207-16, 1994.
10. F. J. Patrick and J. P. Alain, "High accuracy prediction of β-turns and their types using propensities and multiple alignments," Proteins, vol. 59, pp. 828-839, 2005.
11. C. T. Zhang and K. C. Chou, "Prediction of beta-turns in proteins by 1-4 & 2-3 correlation model," Biopolymers, vol. 41, pp. 673-702, 1997.
12. M. J. McGregor, T. P. Flores and M. J. E. Sternberg, "Prediction of β-turns in proteins using neural network," Protein Eng., vol. 2, pp. 521-526, 1989.
13. A. J. Shepherd, D. Gorse, and J. M. Thornton, "Prediction of the location and type of beta-turns in proteins using neural networks," Protein Sci, vol. 8, pp. 1045-55, 1999.
14. H. Kaur and G. P. Raghava, "An evaluation of beta-turn prediction methods," Bioinformatics, vol. 18, pp. 1508-14, 2002.
15. S. Kim, "Protein beta-turn prediction using nearest-neighbor method," Bioinformatics, vol. 20, pp. 40-4, 2004.
16. Q. Zhang, S. Yoon, and W. J. Welsh, "Improved method for predicting beta-turn using support vector machine," Bioinformatics, vol. 21, pp. 2370-4, 2005.
17. C. Cortes and V. Vapnik, "Support vector networks," Machine Learning, vol. 20, pp. 273-293, 1995.
18. V. Vapnik, Statistical Learning Theory. New York: John Wiley and Sons, Inc., 1998.
19. L. H. Wang, J. Liu, Y. F. Li, and H. B. Zhou, "Predicting protein secondary structure by a support vector machine based on a new coding scheme," Genome Inform Ser Workshop Genome Inform, vol. 15, pp. 181-90, 2004.
20. S. Hua and Z. Sun, "A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach," J Mol Biol, vol. 308, pp. 397-407, 2001.
21. H. Kim and H. Park, "Protein secondary structure prediction based on an improved support vector machines approach," Protein Eng, vol. 16, pp. 553-60, 2003.
22. M. N. Nguyen and J. C. Rajapakse, "Multi-class support vector machines for protein secondary structure prediction," Genome Inform Ser Workshop Genome Inform, vol. 14, pp. 218-27, 2003.
23. H. N. Lin, J. M. Chang, K. P. Wu, T. Y. Sung, and W. L. Hsu, "HYPROSP II-a knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence," Bioinformatics, vol. 21, pp. 3227-33, 2005.
24. D. T. Jones, "Protein secondary structure prediction based on position-specific scoring matrices," J Mol Biol, vol. 292, pp. 195-202, 1999.
25. L. J. McGuffin, K. Bryson, and D. T. Jones, "The PSIPRED protein structure prediction server," Bioinformatics, vol. 16, pp. 404-5, 2000.
26. S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs," Nucleic Acids Res, vol. 25, pp. 3389-402, 1997.
27. C. C. Chang and C. J. Lin, "LIBSVM: a library for support vector machines". Available: http://www.csie.ntu.edu.tw/~cjlin/libsvm
28. E. G. Hutchinson and J. M. Thornton, "PROMOTIF-a program to identify and analyze structural motifs in proteins," Protein Sci, vol. 5, pp. 212-20, 1996.
29. W. Kabsch and C. Sander, "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features," Biopolymers, vol. 22, pp. 2577-637, 1983.