Prediction of Interactiveness between Small Molecules and Enzymes by Combining Gene Ontology and Compound Similarity

Journal of Computational Chemistry

Volumn 31, Issue 8, 2010, Pages 1766-1776

  Chen, Lei ^a,b   Qian, Ziliang ^c   Fen, Kaiyan ^d   Cai, Yudong ^e  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

^c MAX PLANCK INSTITUTE   (Germany)

^d UNIVERSITY OF MANCHESTER   (United Kingdom)

^e SHANGHAI UNIVERSITY   (China)

Author keywords

Blast; Compound similarity; Functional domain composition; Gene ontology; Metabolic pathway; Molecule enzyme couple; Nearest neighbor algorithm (nna); Simple majority voting system

Indexed keywords

FUNCTIONAL DOMAIN COMPOSITION; FUNCTIONAL DOMAINS; GENE ONTOLOGY; METABOLIC PATHWAYS; NEAREST NEIGHBOR ALGORITHM; SIMPLE MAJORITY;

ALGORITHMS; CATALYSTS; DIES; ENZYMES; MATHEMATICAL MODELS; METABOLISM; MOLECULES; ONTOLOGY; STATISTICAL TESTS; VOTING MACHINES;

FORECASTING;

ENZYME; ORGANIC COMPOUND;

ALGORITHM; ARTICLE; CHEMISTRY; CONFORMATION; GENETIC DATABASE; GENETICS; METABOLISM; MOLECULAR WEIGHT;

ALGORITHMS; DATABASES, GENETIC; ENZYMES; MOLECULAR CONFORMATION; MOLECULAR WEIGHT; ORGANIC CHEMICALS;

EID: 77952351365     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21467     Document Type: Article

References (49)

1. Metzler, D. E. Biochemistry: The Chemical Reactions of Living Cells; Academic Press: London, 1977.
2. Marchand-Geneste, N.; Watson, K. A.; Alsberg, B. K.; King, R. D. J Med Chem 2002, 45, 399.
3. Lu, L.; Shi, X. H.; Li, S. J.; Xie, Z. Q.; Feng, Y. L.; Lu, W. C.; Li, Y. X.; Li, H. P.; Cai, Y. D. Mol Divers (in press).
4. Lu, L. Y.; Qian, Z. L.; Shi, X. H.; Li, H. P.; Cai, Y. D.; Li, Y. X. Mol Divers (in press).
5. Li, W. J.; Lin, K.; Feng, K. Y.; Cai, Y. D. Mol Divers 2008, 12, 171.
6. Cai, Y. D.; Qian, Z. L.; Lu, L.; Feng, K. Y.; Meng, X.; Niu, B.; Zhao, G. D.; Lu, W. C. Mol Divers 2008, 12, 131.
7. Niu, B.; Jin, Y. H.; Feng, K. Y.; Lu, W. C.; Cai, Y. D.; Li, G. Z. Mol Divers 2008, 12, 41.
8. Chou, K. C.; Cai, Y. D.; Zhong, W. Z. EXCLI J 2006, 5, 55.
9. Wishart, D. S.; Tzur, D.; Knox, C.; Eisner, R.; Guo, A. C.; Young, N.; Cheng, D.; Jewell, K.; Arndt, D.; Sawhney, S.; Fung, C.; Nikolai, L.; Lewis, M.; Coutouly, M. A.; Forsythe, I.; Tang, P.; Shrivastava, S.; Jeroncic, K.; Stothard, P.; Amegbey, G.; Block, D.; Hau, D. D.; Wagner, J.; Miniaci, J.; Clements, M.; Gebremedhin, M.; Guo, N.; Zhang, Y.; Duggan, G. E.; MacInnis, G. D.; Weljie, A. M.; Dowlatabadi, R.; Bamforth, F.; Clive, D.; Greiner, R.; Li, L.; Marrie, T.; Sykes, B. D.; Vogel, H. J.; Querengesser L. Nucl Acids Res 2007, 35, 521.
10. Sarah, A. T.; Stuart, C. G. R.; Janet, M. T.; Monica, R.; Julian, G.; Cyrus, C. Trends Biotech 2001, 19, 482.
11. Cai, Y. D.; Muldoon, M. MIMS EPrint 2007, 1.
12. Quinlan, R. C4.5: Programs for Machine Learning; Morgan Kaufmann; San Mateo, 1993.
13. Bishop, C. M. Neural Networks for Pattern Recognition; Oxford Press: London, 1995.
14. Cristianini, N.; Shawe-Taylor, J. An Introduction to Support Vector Machines; Cambridge University Press: Cambridge, 2000.
15. Vapnik, V. Statistical Learning Theory; Wiley; New York, 1998.
16. Niu, B.; Jin, Y. H.; Lu, L.; Fen, K. Y.; Gu, L.; He, Z. S.; Lu, W. L.; Li, Y. X.; Cai, Y. D. Mol Divers 2009, 13, 313.
17. James, C. A.; Weininger, D.; Delany, J. Daylight Theory Manual 4.71; Daylight Chemical Information Systems, Inc.: Irvine, 2000.
18. Mcgregor, M. J.; Paliai, P. V. J Chem Inf Comput Sci 1997, 37, 443.
19. MDC MACCS Keys; MDL Information Systems Inc.: San Leandro, CA.
20. Hattori, M.; Okuno, Y.; Goto, S.; Kanehisa, M. J Am Chem Soc 2003, 125, 11853.
21. Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. J Mol Biol 1990, 215, 403.
22. Ashburner, M.; Ball, C. A.; Blake, J. A.; Botstein, D.; Butler, H.; Cherry, J. M.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.; Hill, D. P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock G. Nat Genet 2000, 25, 25.
23. Chou, K. C.; Cai, Y. D. J Biol Chem 2002, 277, 45765.
24. Murvai, J.; Vlahovicek, K.; Barta, E.; Pongor, S. Nucl Acids Res 2001, 29, 58.
25. Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Birney, E.; Biswas, M.; Bucher, P.; Cerutti, L.; Corpet, F.; Croning, M. D. R.; Durbin, R.; Falquet, L.; Fleischmann, W.; Gouzy, J.; Hermjakob, H.; Hulo, N.; Jonassen, I.; Kahn, D.; Kanapin, A.; Karavidopoulou, Y.; Lopez, R.; Marx, B.; Mulder, N. J.; Oinn, T. M.; Pagni, M.; Servant, F.; Sigrist, C. J. A.; Zdobnov, E. M. Nucl Acids Res 2001, 29, 37.
26. Izrailev, S.; Farnum, M. A. Proteins 2004, 57, 711.
27. Bender, A.; Jenkins, J. L.; Glick, M.; Deng, Z.; Nettles, J. H.; Davies, J. W. J Chem Inf Model 2006, 46, 2445.
28. Keiser, M. J.; Roth, B. L.; Armbruster, B. N.; Ernsberger, P.; Irwin, J. J.; Shoichet, B. K. Nat Biotechnol 2007, 25, 197.
29. Goto, S.; Nishioka, T.; Kanehisa, M. Bioinformatics 1998, 14, 591.
30. Kanehisa, M.; Goto, S.; Hattori, M.; Aoki-Kinoshita, K. F.; Itoh, M.; Kawashima, S.; Katayama, T.; Araki, M.; Hirakawa, M. Nucl. Acids Res 2006, 34, 354.
31. Bron, C.; Kerbosch, J. Commun ACM 1973, 16, 575.
32. Jaccard, P. N Phytol 1912, 11, 37.
33. Watson, G. A. SIAM J Sci Stat Comput 1983, 4, 748.
34. Chou, K. C.; Cai, Y. D. Biochem Biophys Res Commun 2004, 321, 1007.
35. Jia, P. L.; Qian, Z. L.; Zeng, Z. B.; Cai, Y. D.; Li, Y. X. Biochem Biophys Res Commun 2007, 357, 366.
36. Yu, X. J.; Wang, C.; Li, Y. X. BMC Bioinformatics 2006, 7, 187.
37. Xu, X. C.; Yu, D.; Fang, W.; Cheng, Y. S.; Qian, Z. L.; Lu, W. C.; Cai, Y. D.; Feng, K. Y. J Proteome Res 2008, 7, 4521.
38. Hannenhalli, S. S.; Russell, R. B. J Mol Biol 2000, 303, 61.
39. Jones, C. E.; Baumann, U.; Brown, A. L. BMC Bioinformatics 2005, 6, 272.
40. Chou, K. C.; Cai, Y. D. Biochem Biophys Res Commun 2004, 320, 1236.
41. Carroll, S.; Pavlovic, V. Bioinformatics 2006, 22, 1871.
42. Chou, K. C.; Cai, Y. D. Biochem Biophys Res Commun 2005, 327, 845.
43. Chou, K. C.; Cai, Y. D. Bioinformatics 2005, 21, 944.
44. Salzberg, S.; Cost, S. J Mol Biol 1992, 227, 371.
45. Chen, L.; Lu, L.; Feng, K.; Li, W.; Song, J.; Zheng, L.; Yuan, Y.; Zeng, Z.; Feng, K.; Lu, W.; Cai, Y. J Comput Chem 2009, 30, 2248.
46. Cai, C. Z.; Wang, W. L.; Sun, L. Z.; Chen, Y. Z. Math Biosci 2003, 185, 111.
47. Ding, C. H. Q.; Dubchak, I. Bioinformatics 2001, 17, 349.
48. Baldi, P.; Brunak, S.; Chauvin, Y.; Anderson, C. A. F.; Nielsen, H. Bioinformatics 2000, 16, 412.
49. Du, P. F.; Li, Y. D. BMC Bioinformatics 2006, 7, 518.