An information-theoretic approach to the prediction of protein structural class

Journal of Computational Chemistry

Volumn 31, Issue 6, 2010, Pages 1201-1206

  Xiaoqi, Zheng ^a   Chun, L I ^b   Jun, Wang ^a,c  

^a SHANGHAI NORMAL UNIVERSITY   (China)

^b BOHAI UNIVERSITY   (China)

^c Scientific Computing Key Laboratory   (China)

Author keywords

Fuzzy k nearest neighbor algorithm; Jackknife analysis; Protein structural class prediction; Sequence decomposition; Symbol sequence complexity

Indexed keywords

DECOMPOSITION TECHNIQUE; EXISTING METHOD; FUZZY K-NEAREST NEIGHBOR ALGORITHM; INFORMATION-THEORETIC APPROACH; K NEAREST NEIGHBOR ALGORITHM; PROTEIN SEQUENCES; STRUCTURAL CLASS; SYMBOL SEQUENCES; THEORETICAL APPROACH;

FEATURE EXTRACTION; FORECASTING; FUZZY CLUSTERING; INFORMATION THEORY; PROTEINS;

CLUSTERING ALGORITHMS;

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CHEMICAL MODEL; CHEMISTRY; CLASSIFICATION; INFORMATION SCIENCE; METHODOLOGY; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; INFORMATION THEORY; MODELS, CHEMICAL; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 77950588824     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21406     Document Type: Article

References (69)

1. Chou, K. C. Curr Protein Pept Sci 2000, 1, 171.
2. Levitt, M.; Chothia, C. Nature 1976, 261, 552.
3. Bu, W. S.; Feng, Z. P.; Zhang, Z.; Zhang, C. T. Eur J Biochem, 1999, 266, 1043.
4. Jin, L.; Fang, W.; Tang, H. Comput Bio Chem 2003, 27, 373.
5. Sun, X. D.; Huang, R. B. Amino Acids 2006, 30, 469.
6. Luo, R. Y.; Feng, Z. P.; Liu, J. K. Eur J Biochem 2002, 269, 4219.
7. Chou, K. C.; Cai, Y. D. Biochem Biophys Res Commun 2004, 321, 1007.
8. Klein, P.; Delisi, C. Biopolymers 1986, 25, 1659.
9. Nakashima, H.; Nishikawa, R.; Ooi, T. J Biochem 1986, 99, 153.
10. Chou, R. C.; Zhang, C. T. J Bio Chem 1994, 269, 22014.
11. Dubchak, I.; Muchnik, I.; Holbrook, S. R.; Kim, S. H. Proc Natl Acad Sci USA 1995, 92, 8700.
12. Dubchak, I.; Muchnik, I.; Mayor, C.; Dralyuk, i.; Kim, S. H. Proteins 1999, 35, 401.
13. Metfessel, B.; Saurugger, P.; Connelly, P.; Rich, S. Protein Sci 1993, 2, 1171.
14. Cai, Y. D.; Zhou, G. P. Biochimie 2000, 82, 783.
15. Eisenhaber, F.; Frömmel, C.; Argos, P. Proteins 1996, 25, 169.
16. Chou, K. C.; Maggiora, G. M. Protein Eng 1998, 11, 523.
17. Wang, Z. X.; Yuan, Z. Proteins 2000, 38, 165.
18. Cai, Y. D.; Liu, X. J.; Xu, X. B.; Zhou, G. P. BMC Bioinformatics 2001, 2, 1.
19. Feng, K. Y.; Cai, Y. D.; Chou, K. C. Biochem Biophys Res Commun 2005, 334, 213.
20. Chou, K. C.; Shen, H. B. Anal Biochem 2007, 370, 1.
21. Chou, R. C. Proteins Struct Funct Genet 2001, 43, 246.
22. Chou, K. C. Bioinformatics 2005, 21, 10.
23. Ding, Y. S.; Zhang, T. L.; Chou, K. C. Protein Peptide Lett 2007, 14, 811.
24. Zhang, T. L.; Ding, Y. S.; Chou, K. C. J Theor Biol 2008, 250, 186.
25. Xiao, X.; Wang, P.; Chou, K. C. J Theor Biol 2008, 254, 691.
26. Xiao, X.; Shao, S.; Ding, Y.; Huang, Z.; Huang, Y.; Chou, K. C. Amino Acids 2005, 28, 57.
27. Chou, K. C.; Shen, H. B. J Proteome Res 2007, 6, 1728.
28. Chou, K. C.; Shen, H. B. Biochem Biophys Res Commun 2006, 347, 150.
29. Shen, H. B.; Chou, R. C. Biochem, Biophys Res Commun, 2005, 337, 752.
30. Mundra, P.; Rumar, M.; Rumar, K. K.; Jayaraman, V. K.; Kulkami, B. D. Pattern Recogn Lett 2007, 28, 1610.
31. Du, P.; Li, Y. BMC Bioinformatics 2006, 7, 518.
32. Chou, K. C.; Cai, Y. D. Proteins Struct Funct Genet 2003, 53, 282.
33. Mondai, S.; Bhavna, R.; Mohan Babu, R.; Ramakumar, S. J Theor Biol 2006, 243, 252.
34. Chou, K. C.; Shen, H. B. Biochem, Biophys Res Commun, 2007, 360, 339.
35. Shen, H. B.; Chou, K. C. Biochem Biophys Res Commun 2007, 364, 53.
36. Shen, H. B.; Chou, K. C. Bioinformatics 2006, 22, 1717.
37. Chou, K. C.; Shen, H. B. Biochem, Biophys Res Commun, 2007, 357, 633.
38. Gonzalez-Diaz, H.; Gonzalez-Diaz, Y.; Santana, L.; Ubeira, F. M.; Uriarte, E. Proteomics 2008, 8, 750.
39. Lempel, A.; Ziv, J. IEEE T Inform Theory 1976, 22, 75.
40. Ziv, J.; Lempel, A. IEEE T Inform Theory 1977, 23, 337.
41. Ziv, J.; Lempel, A. IEEE T Inform Theory 1978, 24, 530.
42. Otu, H. H.; Sayood, K. Bioinformatics 2003, 19, 2122.
43. Orlov, Y. L.; Potapov, V. N. Nucleic Acids Res 2004, 32, 628.
44. Wang, J.; Zheng, X. J Theor Biol 2008, 250, 382.
45. Hu, J.; Gao, J.; Principe, J. IEEE Trans Biomed Eng 2006, 53, 2606.
46. Duda, R. O.; Hart, P. E.; Stork, D. G. Pattern Classification, 2nd ed.; Wiley: New York, 2000.
47. Keller, J. M.; Gray, M. R.; Givens, J. A. IEEE Trans Syst Man Cybern 1985, 15, 580.
48. Bezdek, J. C. J Intel Fuzzy Sys 1993, 1, 1.
49. Chou, K. C. Biochem Biophys Res Commun, 1999, 264, 216.
50. Cai, Y. D.; Liu, X. J.; Xu, X. B.; Chou, K. C. Comput Chem, 2002, 26, 293.
51. Chen, C.; Tian, Y. X.; Zou, X. Y.; Cai, P. X.; Mo, J. Y. J Theor Biol 2006, 243, 444.
52. Shen, H. B.; Yang, J.; Liu, X. J.; Chou, R. C. Biochem, Biophys Res Commun 2005, 334, 577.
53. Cai, Y. D.; Feng, R. Y.; Lu, W. C.; Chou, K. C. J Theor Biol 2006, 238, 172.
54. Xiao, X.; Shao, S. H.; Huang, Z. D.; Chou, K. C. J Comput Chem 2006, 27, 478.
55. Zhang, T. L.; Ding, Y. S. Amino Acids 2007, 33, 623.
56. Lin, H.; Li, Q. Z. J Comput Chem 2007, 28, 1463.
57. Chou, K. C.; Zhang, C. T. Crit Rev Biochem, Mol 1995, 30, 275.
58. Chou, K. C.; Shen, H. B. Nat Protoc 2008, 3, 153.
59. Zhou, G. P.; Assa-Munt, N. Proteins Struct Funct Genet 2001, 44, 57.
60. Zhou, X. B.; Chen, C.; Li, Z. C.; Zou, X. Y. J Theor Biol 2007, 248, 546.
61. Zhang, G. Y.; Fang, B. S. J Theor Biol 2008, 253, 310.
62. Lin, H. J Theor Biol 2008, 252, 350.
63. Zhang, G. Y.; Li, H. C.; Fang, B. S. Protein Peptide Lett 2008, 15, 1132.
64. Jiang, X.; Wei, R.; Zhang, T. L.; Gu, Q. Protein Peptide Lett 2008, 15, 392.
65. Li, F. M.; Li, Q. Z. Protein Peptide Lett 2008, 15, 612.
66. Lin, H.; Ding, H.; Feng-Biao Guo, F. B.; Zhang, A. Y.; Huang, J. Protein Peptide Lett 2008, 15, 739.
67. Wang, T.; Yang, J.; Shen, H. B.; Chou, R. C. Protein Peptide Lett 2008, 15, 915.
68. Zhou, G. P. J Protein Chem 1998, 17, 729.
69. Cao, Y. F.; Liu, S.; Zhang, L. D.; Qin, J.; Wang, J.; Tang, K. X. BMC Bioinformatics 2006, 7, 1.