Recursive partitioning analysis of a large structure-activity data set using three-dimensional descriptors

Journal of Chemical Information and Computer Sciences

Volumn 38, Issue 6, 1998, Pages 1054-1062

  Chen, Xin ^a,b   Rusinko III, Andrew ^b   Young, S Stanley ^b  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b GLAXOSMITHKLINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000128084     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci980089g     Document Type: Article

References (36)

1. Patents pending. We have patents pending on these methods.
2. Gallop, M. A.; Barrett, R. W.; Dower, W. J.; Bodor, S. P. A.; Gordon, E. M. Applications of Combinatorial Technologies to Drug Discovery. 1. Background and Peptide Combinatorial Libraries. J. Med. Chem. 1994, 37, 1233-1251.
3. Gordon, E. M.; Barrett, R. W.; Dower, W. J.; Fodor, S. P. A.; Gallop, M. A. Applications of Combinatorial Technologies to Drug Discovery. 2. Combinatorial Organic Synthesis, Library Screening Strategies, and Future Directions. J. Med. Chem. 1994, 37, 1385-1401.
4. Kubunyi, H. QSAR: Hansch Analysis and Related Approaches; VCH: 1993.
5. Hansch, C.; Leo, A. Exploring QSAR. Fundamentals and Applications in Chemistry and Biology; American Chemical Society; 1995.
6. King, R. D.; Muggleton, S.; Lewis, R. A.; Sternberg, M. J. Drug Design by Machine Learning: the Use of Inductive Logic Programming to Model the Structure-Activity Relationships of Trimethoprim Analogues Binding to Dihydrofolate Reductase. PNAS 1992, 89, 11322-11326.
7. King, R. D.; Muggleton, S.; Srinivasan, A.; Sternberg, M. J. Structure-Activity Relationships Derived by Machine Learning: the Use of Atoms and Their Bond Connectivities to Predict Mutagenicity by Inductive Logic Programming. PNAS 1996, 93, 438-442.
8. Klopman, G. Artificial Intelligence Approach to Structure-Activity Studies. Computer Automated Structure Evaluation of Biological Activity of Organic Molecules. J. Am. Chem. Soc. 1984, 106, 7315-7321.
9. Klopman, G. MULTICASE. 1. A Hierarchical Computer Automated Structure Evaluation Program. Quant. Struct.-Act. Relat. 1992, 11, 176-184.
10. 9 Full Factorial Chemical Library. J. Med. Chem. 1995, 38, 2784-2788.
11. Young, S. S.; Hawkins, D. M. Using Recursive Partitioning to Analyze a Large SAR Data Set. SAR QSAR Env. Res. 1998, 8, 183-193.
12. Hawkins, D. M.; Young, S. S.; Rusinko, A. Analysis of a Large Structure-Activity Data Set Using Recursive Partitioning. Quant. Struct.-Act. Relat. 1997, 16, 1-7.
13. Rusinko, A.; Farmen, M. W.; Lambert, C. G.; Brown, P. L.; Young, S. S. SCAM: Statistical Classification of Activities of Molecules Using Recursive Partitioning. J. Am. Chem. Soc. To be submitted.
14. Willett, P. Similarity and Clustering in Chemical Information Systems; Research Studies Press: Letchworth, 1987.
15. Barnard, J. M.; Downs, G. A. Clustering of Chemical Structures on the Basis of 2-D Similarity Measures. J. Chem. Inf. Comput. Sci. 1992, 32, 644-649.
16. Downs, G. M.; Wilett, P. In Advanced Computer-Assisted Techniques in Drug Discovery; van de Waterbeemd, H., Ed.; VCH: Weinheim; 1994; Vol. 3.
17. Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. Atom Pairs as Molecular Features in Structure-Activity Studies: Definition and Applications. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
18. Nilakantan, R.; Bauman, N.; Dixon, J. S.; Venkataraghavan, R. Topological Torsion: a New Molecular Descriptor for SAR Applications. Comparison with Other Descriptors. J. Chem. Inf. Comput. Sci. 1987, 27, 82-85.
19. Nilikantan, R.; Bauman, N.; Venkataraghavan, R. New Method for Rapid Characterization of Molecular Shapes: Application in Drug Design. J. Chem. Inf. Comput. Sci. 1993, 33, 79-85.
20. Miller, M.; Schneider, J.; Sathyanarayana, B. K.; Toth, M. V.; Marshal, G. R.; Clawson, L.; Selk, L.; Kent, S. B. H.; Wlodawer, A. Structure of a Complex of Synthetic HIV-1 Protease with a Substrate-Based Inhibitor at 2.3 A Resolution. Science 1989, 246, 1149-1152.
21. Kubinyi, H. 3D QSAR in Drug Design: Theory, Methods, and Applications; ESCOM Science Publishers: Leiden, 1993.
22. Cramer, R. D.; Patterson, D. E.; Bruce, J. D. Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 10, 5959-5967.
23. Barnum, D.; Greene, J.; Smellie, A.; Sprague, P. Identification of Common Functional Configurations Among Molecules. J Chem. Inf. Comput. Sci. 1996, 36, 563-571.
24. 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. Comp. Sci 1996, 36, 572-584.
25. CONCORD. A Program for the Rapid Generation of High Quality Approximate 3-Dimensional Molecular Structures; The University of Texas at Austin and Tripos Associates: St. Louis, MO.
26. MACCS-II Manual, Molecular Design Ltd.: San Leandro, CA.
27. SYBYL Manual; Tripos Associate Inc.: St. Louis, MO.
28. Nicklaus, M. C.; Wang, S.; Driscoll, J. S.; Milne, W. A. Conformational Changes of Small Molecules Binding to Proteins. Bioorg. Med. Chem. 1995, 3, 411-428.
29. Clark, M.; Cramer, R. D.; Opdenbosch, N. V. Validation of the General Purpose Tripos 5.2 Force Field. J. Comput. Chem. 1989, 8, 982-1012.
30. Hawkins, D. M.; Kass, G. V. In Topics in Applied Multivariate Analysis; Hawkins, D. H., Ed.; Cambridge University Press: 1982; p 269.
31. Miller, R. G. Simultaneous Statistical Inference; Springer-Verlag: New York, 1981.
32. SAS Manual; SAS Institute Inc.: Gary, NC.
33. Nelson, S. D.; Mitchell, J. R.; Timbrell, J. A.; Snodgrass, W. R.; Corcoran, G. B., III. Soniazid and Iproniazid: Activation of Metabolites to Toxic Intermediates in Man and Rat. Science 1976, 193, 901-903.
34. Maycock, A. L.; Abeles, R. H.; Salach, J. I.; Singer, T. P. The Structure of the Covalent Adduct Formed by the Interaction of 3-dimethylamino-1-propyne and the Flavine of Mitochondrial Amine Oxidase. Biochemistry 1976, 15, 114-125.
35. Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A. A Fast New Approach to Pharmacophore Mapping and Its Application to Dopaminergiic and Benzodiazepine Agonists. J. Comp.-Aided Mol. Des. 1993, 7, 83-102.
36. Johnson, C. L. Quantitative Structure-Activity Studies on Monoamine Oxidase Inhibitors. J Med. Chem. 1976, 19, 600-605.