Simple idea to generate fragment and pharmacophore descriptors and their implications in chemical informatics

Journal of Chemical Information and Modeling

Volumn 49, Issue 3, 2009, Pages 543-548

  Catana, Cornel ^a  

^a EMD SERONO INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; INFORMATICS; MOLECULES;

ATOMIC DESCRIPTORS; CHEMICAL INFORMATICS; MODEL PERFORMANCE; MULTIPLE INSTANCES; PARTITION COEFFICIENT; PHARMACOPHORE DESCRIPTORS; PHARMACOPHORES; TRADITIONAL VALUES;

PHARMACODYNAMICS;

ARTICLE; DRUG DEVELOPMENT; INFORMATION SYSTEM; SENSITIVITY AND SPECIFICITY;

DRUG DISCOVERY; INFORMATION SYSTEMS; SENSITIVITY AND SPECIFICITY;

EID: 65249134411     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci800339p     Document Type: Article

References (20)

1. Bender, A.; Glen, R. C. Molecular similarity: A key techniques in molecular informatics. Org. Biomol. Chem. 2004, 2, 3204-3218.
2. Conne, M. M.; Venkataraghavan, R.; McLafferty, F. W. Computer-aided interpretation of mass spectra. 20. Molecular structure comparison program for the identification of maximal common substructures. J. Am. Chem. Soc. 1977, 99, 7668-7671.
3. Free, S. M.; Wilson, J. W. A mathematical contribution to structure-activity studies. J. Med. Chem. 1964, 53, 395-399.
4. Barnard, J. M. Substructure searching methods: Old and new. J. Chem. Inf. Comput. Sci. 1993, 33, 532-538.
5. Takahashi, Y.; Sukekawa, M.; Sasaki, S. Automatic identification of molecular similarity using reduced-graph representation of chemical structure. J. Chem. Inf. Comput. Sci. 1992, 32, 639-643.
6. 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.
7. Faulon, J. L.; Visco, 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.
8. Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Molecular similarity searching using atom environments, information-based feature selection, and a naïve bayesian classifier. J. Chem. Inf. Comput. Sci. 2004, 44, 170-178.
9. a and logD. J. Chem. Inf. Comput. Sci. 2002, 42, 796-805.
10. a by molecular tree structured fingerprints and PLS. J. Chem. Inf. Comput. Sci. 2003, 43, 870-879.
11. Hall, H. L.; Mohney, B. The electrotopological state: Structure information at the atomic level for molecular graphs. J. Chem. Inf. Comput. Sci. 1991, 31, 76-82.
12. Wildman, A. S.; Crippen, M. G. Prediction of physicochemical parameters by atomic contributions. J. Chem. Inf. Comput. Sci. 1999, 39, 868-873.
13. Molecular Operating Environment (MOE), version 2008; Chemical Computing Group Inc.: Montreal, Canada, 2008.
14. Pipeline Pilot, version 6.0; Accelrys: San Diego, CA, 2008.
15. Burges, C. J. C. A tutorial on support vector machines for pattern recognition. Data Min. Knowledge Discovery 1998, 2, 121-167.
16. Breiman, L. Random forest. Machine Learning 2001, 45, 5-32.
17. The Comprehensive R Archive Network, http://cran.r-project.org (accessed March 27, 2008).
18. Li, Q.; Jorgensen, S. F.; Oprea, T.; Brunak, S.; Taboureau, O. hERG Classification model based on a combination of support vector machine method and GRIND descriptors. Mol. Pharm. 2007, 5 (1), 117-127.
19. Williams, C.; Schreyer, S. K. Reverse Fingerprinting and Mutual Information-Based Activity Labeling and Scoring (MIBALS); Chemical Computing Group Inc.: Montreal, Canada (to be published).
20. Joachims, T. A Support Vector Method for Multivariate Performance Measures. Presented at the International Conference on Machine Learning [Online], Bonn, Germany, 2005. Support Vector Machine for Multivariate Performance Measures Web Site. http://svmlight. joachims.org (accessed Oct 13, 2008).