Bayesian inference network significantly improves the effectiveness of similarity searching using multiple 2D fingerprints and multiple reference structures

QSAR and Combinatorial Science

Volumn 28, Issue 11-12, 2009, Pages 1537-1545

  Abdo, Ammar ^a   Salim, Naomie ^a  

^a UNIVERSITI TEKNOLOGI MALAYSIA   (Malaysia)

Author keywords

Bayesian inference network; Drug discovery; Inference network; Multiple reference structures; Similarity searching; Virtual screening

Indexed keywords

ARTICLE; BAYES THEOREM; BAYESIAN INFERENCE NETWORK; BIOLOGICAL ACTIVITY; COMPUTER PROGRAM; MOLECULAR IMPRINTING; MOLECULAR MODEL; PRIORITY JOURNAL; PROBABILITY; STRUCTURE ACTIVITY RELATION;

EID: 76049101013     PISSN: 1611020X     EISSN: 16110218     Source Type: Journal    
DOI: 10.1002/qsar.200960062     Document Type: Article

References (32)

1. M. A. Johnson, G. M. Maggiora, Concepts and Application of Molecular Similarity, Wiley, New York 1990.
2. P. Willett, J. M. Barnard, G. M. Downs, J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
3. A. Bender, R. C. Glen, Org. Biomol. Chem. 2004, 2, 3204-3218.
4. P. Willett, J. Med. Chem. 2005, 48, 4183-4199.
5. N. E. Shemetulskis, D. Weininger, C. J. Blankley, J. J. Yang, C. Humblet, J. Chem. Inf. Comput. Sci. 1996, 36, 862-871.
6. R. P. Sheridan, J. Chem. Inf. Comput. Sci. 2000, 40, 1456-1469.
7. L. Xue, J. W. Godden, F. L. Stahura, J. Bajorath, J. Chem. Inf. Comput. Sci. 2003, 43, 1218-1225.
8. A. Schuffenhauer, P. Floersheim, P. Acklin, E. Jacoby, J. Chem. Inf. Comput. Sci. 2003, 43, 391-405.
9. J. Hert, P. Willett, D. J. Wilton, P. Acklin, K. Azzaoui, E. Jacoby, A. Schuffenhauer, Org. Biomol. Cheem. 2004, 2, 3256-3266.
10. J. Hert, P. Willett, D. J. Wilton, P. Acklin, K. Azzaoui, E. Jacoby, A. Schuffenhauer, J. Chem. Inf. Comput. Sci. 2004, 44, 1177-1185.
11. J. Hert, P. Willett, D. J. Wilton, P. Acklin, K. Azzaoui, E. Jacoby, A. Schuffenhauer, J. Chem. Inf. Model. 2006, 46, 462-470.
12. Ajay, W. P. Walters, M. A. Murcko, J. Med. Chem. 1998, 41, 3314-3324.
13. G. Harper, J. Bradshaw, J. C. Gittins, D. V. S. Green, A. R. Leach, J. Chem. Inf. Comput. Sci. 2001, 41, 1295-1300.
14. B. Chen, R. Harrison, G. Papadatos, P. Willett, D. Wood, X. Lewell, P. Greenidge, N. Stiefl, J. Comput. Aided Mol. Des. 2007, 21, 53-62.
15. X. Xia, E. G. Maliski, P. Gallant, D. Rogers, J. Med. Chem. 2004, 47, 4463-4470.
16. M. Vogt, J. Bajorath, Chem. Biol. Drug Des. 2008, 71, 8-14.
17. H. Geppert, T. Horváth, T. Gärtner, S. Wrobel, J. Bajorath, J. Chem. Inf. Model. 2008, 48, 742-746.
18. A. Abdo, N. Salim, QSAR Comb. Sci. 2009, 28, 654-663.
19. S. K. Kearsley, S. Sallamack, E. M. Fluder, J. D. Andose, R. T. Mosley, R. P. Sheridan, J. Chem. Inf. Comput. Sci. 1996, 36, 118-127.
20. R. P. Sheridan, M. D. Miller, D. J. Underwood, S. K. Kearsley, J. Chem. Inf. Comput. Sci. 1996, 36, 128-136.
21. L. Xue, J. W. Godden, J. Bajorath, J. Chem. Inf. Computer Sci. 2000, 40, 1227-1234.
22. L. Xue, F. L. Stahura, J. W. Godden, J. Bajorath, J. Chem. Inf. Computer Sci. 2001, 41, 394-401.
23. T. Kogej, O. Engkvist, N. Blomberg, S. Muresan, J. Chem. Inf. Model. 2006, 46, 1201-1213.
24. A. Abdo, N. Salim, ChemMedChem 2009, 4, 210-218.
25. A. Abdo, N. Salim, in Adv. Computer Theory Eng, 2008. ICACTE '08, Int. Conf. IEEE 2008, pp. 408-412.
26. A. Abdo, N. Salim, in 237th ACS Nat. Meeting, Salt Lake City, USA 2009.
27. J. Pearl, Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference, Morgan Kaufmann, San Francisco, CA 1988.
28. M. J. McGregor, P. V. Pallai, J. Chem. Inf. Comput. Sci. 1997, 37, 443-448.
29. Pipeline Pilot Basic Chemistry Component Collection, SciTegic Inc., San Diego, CA.
30. MOE (Molecular Operating Environment), Chemical Computing Group Inc., Montreal, Canada.
31. MDL Drug Data Report Database, available from MDL Information Systems Inc., at http://www.mdli.com.
32. G.W. Bemis, M. A. Murcko, J. Med. Chem. 1996, 39, 2887-2893.