Comparison of methods for chemical-compound affinity prediction

SAR and QSAR in Environmental Research

Volumn 17, Issue 5, 2006, Pages 497-514

  Koike, A ^a,b  

^a HITACHI LTD   (Japan)

^b Reverse Proteomics Research Institute Co Ltd   (Japan)

Author keywords

Bagging; Boosting; Structure activity relationship; Support vector machine

Indexed keywords

BINDING ENERGY; DRUG THERAPY; FEATURE SELECTION; FORESTRY; GENETIC ALGORITHMS; LIGANDS; PROTEINS;

BAGGING; BOOSTING; COMPARISON OF METHODS; DESCRIPTORS; FEATURE SELECTION METHODS; OVERALL ACCURACIES; PERFORMANCE; STRUCTURE-ACTIVITY RELATIONSHIPS; SUPPORT VECTORS MACHINE; VIRTUAL SCREENING;

SUPPORT VECTOR MACHINES;

EID: 33749384342     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/10629360600934168     Document Type: Article

References (38)

1. C.W. Yap, Y.Z. Chen. J. Chem. Inf. Mod., 45, 982 (2005).
2. H. Li, C. Ung, C. Yap, Y. Xue, Z. Li, Z. Cao, Y. Chen. Chem. Res. Toxicol., 18, 1071 (2005).
3. S.J. Cho, M.A. Hermsmeier. J. Chem. Inf. Comp. Sci., 42, 927 (2002).
4. D.A. Smith, M.J. Acklanda, B.C. Jones. Drug Discov. Today, 2, 479 (1997).
5. J.J. Sutherland, L.A. O'Brien, D.F. Weaver. J. Chem. Inf. Comp. Sci., 43, 1906 (2003).
6. S. Chowdhury, P. Ellis. Curr. Med. Res. Opin., 12, 1985 (2005).
7. G. Klopman, L.M. Shi, A. Ramu. Mol. Pharmacol., 52, 323 (1997).
8. G.M. Keseru. Bioorg. Med. Chem. Lett., 13, 2773 (2003).
9. M. Tobita, T. Nishikawa, R. Nagashima. Bioorg. Med. Chem. Lett., 15, 2886 (2005).
10. A. Cavalli, E. Poluzzi, F. De Ponti, M. Recanatini. J. Med. Chem., 45, 3844 (2002).
11. M. Leopoldo, F. Berardi, N.A. Colabufo, M. Contino, E. Lacvita, M. Niso, R. Perrone, R. Tortorella. J. Med. Chem., 47, 6616 (2004).
12. M.H. Paluchowska, R. Bugno, S. Charakchieva-Minol, A. Wesolowska, E. Chojnacka-Wójcik. Pol. J. Pharmacol., 54, 641 (2002).
13. M.H. Paluchowska, R. Bugno, S. Charakchieva-Minol, A.J. Bojarski, A. Wesolowska. Pol. J. Pharmacol., 53, 369 (2001).
14. J. Boksa, S. Charakchieva-Minol, B. Duszyñska, R. Bugno, A. Klodziñska, E. Tatarczyñska, E. Chojnacka-Wójcik, A.J. Bojarski. Pol. J. Pharmacol., 55, 1013 (2003).
15. G. Chloñ, M. Pawlowski, B. Duszyñska, A. Szaro, E. Tatarczyñska, A. Klodziñska, E. Chojnacka-Wójcik. Pol. J. Pharmacol., 53, 359 (2001).
16. H. Byrtus, M. Pawlowski, B. Duszyñska, A. Wesolowska, E. Chojnacka-Wójcik, A.J. Bojarski. Pol. J. Pharmacol., 53, 395 (2001).
17. J. Boksa, M.J. Mokrosz, S. Charakchieva-Minol, E. Tatarczyñska, A. Klodziñska, A. Wesolowska, S. Misztal. Pol. J. Pharmacol., 53, 501 (2001).
18. A.L. Sabb, R.L. Vogel, M.G. Kelly, Y. Palmer, D.L. Smith, T.H. Andree, L.E. Schechter. Bioorg. Med. Chem. Lett., 11, 1069 (2001).
19. J. Obniska, M. Pawlowski, M. Kolaczkowski, A. Czopek, B. Duszyñska, A. Klodziñska, E. Tatarczyñska, E. Chojnacka-Wójcik. Pol. J. Pharmacol., 55, 556 (2003).
20. M. Dukat, C. Smith, K. Herrick-Davis, M. Teitler, R.A. Glennon. Bioorg. Med. Chem., 12, 2545 (2004).
21. V. Vapnick. The Nature of Statistical Learning Theory, Springer-Verlag, New York (1995).
22. L. Breiman. Mach. Learn., 45, 5 (2001).
23. L. Breiman, P. Spector. Inter. Rev. Stat., 3, 291 (1992).
24. R. Shapire, Theoretical views of boosting and applications. In Proc. of Tenth Int. Conf. Algorithmic Learning Theory, Tokyo, 6-8 Dec (1999).
25. R. Quinlan. C4.5: Programs for Machine Learning, Morgan Kaufmann, San Diego (1993).
26. A. McCallum and K. Nigam. In Proc. of AAAI/ICML-98 Workshop on Learning for Text Categorization, Vol. 41, Madison, Wisconsin, 26-27 July (1998).
27. T.M. Mitchell. Machine Learning, McGraw-Hill, New York (1997).
28. R. Collobert, S. Bengio. J. Mach. Learn. Res., 1, 143 (2001).
29. M. Mitchell. An Introduction to Genetic Algorithms, MIT Press, Cambridge, MA (1996).
30. I. Guyon, J. Weston, S. Barnhill, V. Vapnik. Mach. Learn., 46, 389 (2002).
31. Y. Yang and J.O. Pedersen. In Proc. of the Fourteenth International Conf. on Machine Learning. pp. 412-420, Morgan Kaufmann, San Francisco, CA (1997).
32. R.J. Schalkoff. Pattern Recognition, John Wiley & Sons, Inc., New York (1991).
33. G.A. Bakken, P.C. Jurs. J. Med. Chem., 43, 4534 (2000).
34. D.F. Lewis, S. Modi, M. Dickins. Drug Metab. Rev., 34, 69 (2002).
35. J.M. Kriegl, L. Eriksson, T. Arnhold, B. Beck. Eur. J. Pharm. Sci., 24, 451 (2005).
36. J.M. Yang, T.W. Shen. Proteins, 59, 205 (2005).
37. M. Song, M. Clark. J. Chem. Inf. Model., 46, 392 (2006).
38. Y. Xue, C.W. Yap, L.Z. Sun, Z.W. Cao, J.F. Wang, Y.Z. Chen. J. Chem. Inf. Comput. Sci., 44, 1497 (2004).