Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance

Journal of Chemical Information and Computer Sciences

Volumn 44, Issue 5, 2004, Pages 1708-1718

  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; SIMILARITY SEARCHING ALGORITHM;

ALGORITHMS; CLASSIFICATION (OF INFORMATION); DATABASE SYSTEMS; FEATURE EXTRACTION; INFORMATION MANAGEMENT; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE;

MOLECULAR PHYSICS;

EID: 5544290537     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci0498719     Document Type: Article

References (50)

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 Discov. Today 1998, 3, 160-178.
3. Nikolova, N.; Jaworska, J. Approaches to measure chemical similarity - A review. QSAR Comb. Sci. 2004, 22, 1006-1026.
4. 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.
5. Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. Do Structurally Similar Molecules Have Similar Biological Activity? J. Med. Chem. 2002, 45, 4350-4358.
6. Kubinyi, H. Similarity and dissimilarity: A medicinal chemist's view. Perspect. Drug Discovery Des. 1998, 9-11, 225-252.
7. Kubinyi, H. Chemical similarity and biological activities. J. Braz. Chem. Soc. 2002, 13, 717-726.
8. 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, 1094-1102.
9. Estrada, E.; Uriarte, E. Recent Advances on the Role of Topological Indices in Drug Discovery Research. Curr. Med. Chem. 2001, 8, 1573-1588.
10. 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.
11. Mason, J. S.; Good, A. C.; Martin, E. J. 3D-Pharmacophores in Drug Discovery. Curr. Pharm. Des. 2001, 7, 567-597.
12. Free, S. M., Jr.; Wilson, J. W. A Mathematical Contribution to Structure-Activity Studies. J. Med. Chem. 1964, 7, 395-399.
13. Kubinyi, H. QSAR: Hansch Analysis and Related Approaches. Methods and Principles in Medicinal Chemistry; Mannhold, R., et al., Eds.; VCH: Weinheim, Germany, 1993; Vol. 1.
14. Pastor, M.; Cruciani, G.; McLay, I.; Pickett, S.; Clementi, S. GRid-INdependent descriptors (GRIND): a novel class of alignment-independent three-dimensional molecular descriptors. J. Med. Chem. 2000, 43, 3233-3243.
15. Wagener, M.; Sadowski, J.; Gasteiger, J. Autocorrelation of Molecular-Surface Properties for Modeling Corticosteroid-Binding Globulin and Cytosolic Ah Receptor Activity by Neural Networks. J. Am. Chem. Soc. 1995, 117, 7769-7775.
16. Kauvar, L. M.; Higgins, D. L.; Villar, H. O.; Sportsman, J. R.; Engquist-Goldstein, A. E.; Bukar, R.; Bauer, K. E.; Dilley, H.; Rocke, D. M. Predicting ligang binding to proteins by affinity fingerprinting, Chem. Biol. 1995, 2, 107-118.
17. 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.
18. Baumann, K. Uniform-length molecular descriptors for quantitative structure-property relationships (QSPR) and quantitative structure-activity relationships (QSAR): classification studies and similarity searching. Trends Anal. Chem. 1999, 18, 36-46.
19. Stiefl, N.; Baumann K. Mapping Property Distributions of Molecular Surfaces: Algorithm and Evaluation of a Novel 3D Quantitative Structure-Activity Relationship Technique. J. Chem. Inf. Comput. Sci. 2003, 46, 1390-1407.
20. Jaccard, P. Étude comparative de la distribution florale dans une portion des Alpes et des Jura. Bull. Soc. Vaudoise Sci. Nat. 1901, 37, 547-579.
21. 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.
22. Holliday, J. D.; Salim, N.; Whittle, M.; Willett, P. Analysis and Display of the Size Dependence of Chemical Similarity Coefficients. J. Chem. Inf. Comput. Sci. 2003, 43, 819-828.
23. Dixon, S. L.; Koehler, R. T. The hidden component of size in two-dimensional fragment descriptors: Side effects on sampling in bioactive libraries. J. Med. Chem. 1999, 42, 2887-2900.
24. Flower, D. R. On the Properties of Bit String-Based Measures of Chemical Similarity. J. Chem. Inf. Comput. Sci. 1998, 38, 379-386.
25. Fligner, M. A.; Verducci, J. S.; Blower, P. E. A modification of the Jaccard-Tanimoto similarity index for diverse selection of chemical compounds using binary strings. Technometrics 2002, 44, 110-119.
26. Ginn, C. M. R.; Willett, P.; Bradshaw, J. Combination of molecular similarity measures using data fusion. Perspect. Drug Discovery Des. 2000, 20, 1-16.
27. a and logD. J. Chem. Inf. Comput. Sci. 2002, 42, 796-805.
28. Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Molecular-similarity searching using atom environments, information-based feature selection, and a naive bayesian classifier. J. Chem. Inf. Comput. Sci. 2004, 44, 170-178.
29. Harper, G.; Bradshaw, J.; Gittins, J. C.; Green, D. V. S.; Leach, A. R. Prediction of biological activity for high-throughput screening using binary kernel discrimination. J. Chem. Inf. Comput. Sci. 2001, 41, 1295-1300.
30. Harper, G. The Selection of Compounds for Screening in Pharmaceutical Research. Ph.D. Thesis, University of Oxford, U.K., 1999.
31. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jaooby, E.; Schuffenhauer, A. Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures J. Chem. Inf. Comput. Sci. 2004, 44, 1177-1185.
32. MDL Drug Data Report, MDL ISIS/HOST software, MDL Information Systems, Inc., San Leandro, CA.
33. Brown, R. D.; Martin, Y. C. Use of structure Activity data to compare structure-based clustering methods and descriptors for use in compound selection. J. Chem. Inf. Comput. Sci. 1996, 36, 572-584.
34. 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.
35. 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.
36. Faulon, J. L.; Visco Jr., D. P.; 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.
37. Adamson, O. W.; Cowell, J.; Lynch, M. F.; McLure, A. H. W.; Town, W. G.; Yapp, A. M. Strategic Considerations in the Design of a Screening System for Substructure Searches of Chemical Structure Files. J. Chem. Doc. 1973, 13, 153-157.
38. SciTegic, Inc., San Diego, CA.
39. Quinlan, J. R. Induction of Decision Trees. Mach. Learn. 1986, 1, 81-106.
40. 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.
41. Machine Learning; Mitchell T. M., Ed.; McGraw-Hill: New York, 1997.
42. OpenBabel, http://openbabel.sourceforge.net/.
43. 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.
44. ISIS, Version 2.1.4, Molecular Design Ltd., San Leandro, CA.
45. Daylight, Version 4.62, Daylight Inc., Mission Viejo, CA.
46. Sybyl, Version 6.5.3, HQSAR Module, Tripos Inc., St. Louis, MO.
47. Lessei, 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.
48. Lemmen, C.; Lengauer, T.; Klebe, G. FLEXS: A Method for Fast Flexible Ligand Superposition. J. Med. Chem. 1998, 41, 4502-4520.
49. Briem, H.; Kuntz, I. D. Molecular similarity based on DOCK-generated fingerprints. J. Med. Chem. 1996, 39, 3401-3408.
50. Monks, A., Scudiero, D., Skehan, P., Shoemaker, R., Paull, K., Vistica, D., Hose, C., Langley, J., Cronise, P., Vaigro-Wolff, A., Gray-Goodrich, M., Campbell, H., Mayo, J.; Boyd, M. Feasibility of a high-flux anticancer drug screen using a diverse panel of cultured human tumor cell lines. J. Nat. Cancer Inst. 1991, 83, 757-766.