Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier

Journal of Chemical Information and Computer Sciences

Volumn 44, Issue 1, 2004, Pages 170-178

  Bender, Andreas ^a   Mussa, Hamse Y ^a   Glen, Robert C ^a   Reiling, Stephan ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b SANOFI   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN CLASSIFIERS; FEATURE SELECTION;

ALGORITHMS; BIOCHEMISTRY; CONFORMATIONS; DRUG PRODUCTS; FEATURE EXTRACTION; GRAPHIC METHODS; MOLECULAR PHYSICS; QUERY LANGUAGES;

INFORMATION ANALYSIS;

EID: 1842690601     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci034207y     Document Type: Article

References (33)

1. Concepts and Applications of Molecular Similarity; Johnson, A. M., Maggiora, G. M., Eds.; Wiley: New York, 1990.
2. Walters, W. P. Virtual Screening - An Overview. Drug Discovery Today 1998, 3, 160-178.
3. Patterson. D. E.; Cramer, R. D.: Ferguson, A. M.; Clark, R. D.; Weinberger, L. E. Neighbourhood Behaviour: A Useful Concept for Validation of "Molecular Similarity" Descriptors. J. Med. Chem. 1996, 39, 3049-3059.
4. Martin, Y. C.; Kofron, J. L.: Traphagen, L. M. Do Structurally Similar Molecules Have Similar Biological Activity? J. Med. Chem. 2002, 45, 4350-4358.
5. Downs, G. M.; Willett, P.; Fisanick, W. Similarity Searching and Clustering of Chemical-Structure Databases Using Molecular Property Data. J. Chem. Inf. Comput. Sci. 1994, 34, 4, 1094-1102.
6. Estrada, E.; Uriarte, E. Recent Advances on the Role of Topological Indices in Drug Discovery Research. Curr. Med. Chem. 2001, 8, 1573-1588.
7. Cramer, R. D.; Patterson, D. R.; Bunce, J. D. Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
8. Mason. J. S.; Good, A. C.; Martin, E. J. 3D-Pharmacophores in Drug Discovery. Curr. Pharm. Des. 2001, 7, 567-597.
9. Wegner, J. K.; Zell, A. Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method. J. Chem. Inf. Comput. Sci. 2003, 43, 1077-1084.
10. Quinlan, J. R. Induction of Decision Trees. Machine Learning 1986, 1, 81-106.
11. An Introduction to Chemoinformatics; Leach, A. R., Gillet, V. J., Eds.; Kluwer: Dordrecht, The Netherlands, 2003.
12. Willett, P.; Winterman, V. A. Comparison of Some Measures for the Determination of Intermolecular Structural Similarity Measures of Intermolecular Structural Similarity. Quant. Struct.-Act. Relat. 1986, 5, 18-25.
13. Holliday, J. D.; Hu, C.-Y.; Willett, P. Grouping of Coefficients for the Calculation of Inter-Molecular Similarity and Dissimilarity using 2D Fragment Bit-Strings. Comb. Chem. High Throughput Screening 2002, 5, 155-166.
14. a, and log D. J. Chem. Inf. Comput. Sci. 2002, 42, 796-805.
15. Faulon, J. L. Stochastic Generator of Chemical Structure: 1. Application to the Structure Elucidation of Large Molecules. J. Chem. Inf. Comput. Sci. 1994, 34, 1204-1218.
16. Visco, D. P., Jr.; Pophale R. S.; Rintoul M. D.; Faulon, J. L. Developing a Methodology for an Inverse Quantitative Structure-Activity Relationship Using the Signature Molecular Descriptor. J. Mol. Graphics Modell. 2002, 20, 429-438.
17. Faulon, J. L.; Visco, D. P., Jr.; Pophale, R. S. The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR Studies. J. Chem. Inf. Comput. Sci. 2003, 43, 707-720.
18. Faulon, J. L.; Churchwell, C. J.; Visco, D. P., Jr. The Signature Molecular Descriptor. 2. Enumerating Molecules from Their Extended Valence Sequences. J. Chem. Inf. Comput. Sci. 2003, 43, 721-734.
19. Clark, R. D.; Cramer, R. D.; Van Opdenbosch, N. Validation of the General Purpose Tripos 5.2 Force Field. J. Comput. Chem. 1989, 10, 982-1012.
20. Glen, R. C.; A-Razzak, M. Applications of Rule-Induction in the Derivation of Quantitative Structure-Activity Relationships. J. Comput.-Aided Mol. Des. 1992, 6, 349-383.
21. Machine Learning: Mitchell, T. M., Ed.; McGraw-Hill: New York, 1997.
22. MDL Drug Data Report; MDL ISIS/HOST software, MDL Information Systems, Inc.; San Leandro, CA.
23. Briem, H.; Lessel, U. F. In Vitro and in Silico Affinity Fingerprints; Finding Similarities beyond Structural Classes. Perspect. Drug Discovery Des. 2000, 20, 231-244.
24. OpenBabel, http://openbabel.sourceforge.net/.
25. Cushman, D. W.; Cheung, H. S.; Sabo, E. F.; Ondetti, M. A. Design of Potent Competitive Inhibitors of Angiotensin-Converting Enzyme. Carboxyalkanoyl and Mercaptoalkanoyl Amino Acids. Biochemistry 1977, 16, 5484-5491.
26. Natesh, R.; Schwager, S. L. U.; Sturrock, E. D.; Acharya, K. R. Crystal Structure of the Human Angiotensin-Converting Enzyme-Lisinopril Complex. Nature 2003, 421, 551-554.
27. Rarey, M.; Dixon, J. S. Feature Trees: A New Molecular Similarity Measure Based on Tree Matching. J. Comput.-Aided Mol. Des. 1998, 12, 471-490.
28. ISIS, Version 2.1.4; Molecular Design Ltd.: San Leandro, CA, June 1, 1998.
29. Daylight. Version 4.62; DAYLIGHT Inc.: Mission Viejo, CA, March 5, 1999.
30. Sybyl, Version 6.5.3, HQSAR Module; Tripos Inc.: St. Louis, MO, June 1999.
31. Lessel, U. F.; Briem, H. Flexsim-X: A Method for the Detection of Molecules with Similar Biological Activity. J. Chem. Inf. Comput. Sci. 2000, 40, 246-253.
32. Lemmen, C.; Lengauer, T.; Klebe, G. FLEXS: A Method for Fast Flexible Ligand Superposition. J. Med. Chem. 1998, 41, 4502-4520.
33. Briem, H.; Kuntz, I. D. Molecular Similarity Based on DOCK-Generated Fingerprints. J. Med. Chem. 1996, 39, 3401-3408.