The thirty-one benchmark steroids revisited: Comparative Molecular Moment Analysis (CoMMA) with principal component regression

Quantitative Structure-Activity Relationships

Volumn 19, Issue 3, 2000, Pages 237-246

  Silverman, B David ^a  

^a IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

CoMMA; PCA; PCR; Principal components; Regression; Steroids

Indexed keywords

BINDING ENERGY; COMPUTATIONAL CHEMISTRY; LIPIDS; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS;

COMPARATIVE MOLECULAR MOMENT ANALYSE; MOLECULAR MOMENTS; MOMENT ANALYSIS; PCA; PRINCIPAL COMPONENT REGRESSION; PRINCIPAL COMPONENTS; REGRESSION; STEROID; TRAINING SETS;

MOLECULES;

STEROID;

ARTICLE; BINDING AFFINITY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

EID: 0033935713     PISSN: 09318771     EISSN: None     Source Type: Journal    
DOI: 10.1002/1521-3838(200006)19:3<237::AID-QSAR237>3.0.CO;2-A     Document Type: Article

References (15)

1. Cramer, R.D. III, Patterson, D.E. and Bunce, J.D., Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 110, 5959-5967 (1988).
2. Wagener, M., Sadowski, J. and Gasteiger, J., Autocorrelation of Molecular Surface Properties for Modeling Corticosteroid Binding Globulin and Cystolic Ah Receptor Activity by Neural Networks, J. Am. Chem. Soc. 117, 7769-7775 (1995).
3. Coats, E.A., The CoMFA Steroids as a Benchmark Dataset for Development of 3D QSAR Methods, in: Kubiny, H., Folkers, G. and Martin, Y. C. (Eds.), 3D QSAR in Drug Design, Volume 3 Recent Advances, Kluwer/Escom, Dordrecht 1998, pp. 199-213.
4. Kubinyi, H., A General View on Similarity and QSAR Studies, in: Waterbeemd, H. van de, Testa, B. and Folkers, G., (Eds.), Computer-Assisted Lead Finding and Optimization Current Tools for Medicinal Chemistry, Wiley-VCH, Weinheim 1997, pp. 7-28.
5. Crippen, G.M., Validation of EGSITE2, a Mixed Integer Program for(Deducing Objective Site Models from Experimental Binding Data, J. Med. Chem. 40, 3161-3172 (1997).
6. So, S. and Karplus, M., Three-Dimensional Quantitative Structure-Activity Relationships from Molecular Similarity Matrices and Genetic Neural Networks. 1. Method and Validations, J. Med. Chem. 40, 4347-4359 (1997).
7. Turner, D.B., Willet, P., Ferguson, A.M. and Heritage, T.W., Evaluation of a novel molecular vibration-based descriptor (EVA) for QSAR studies: 2. Model validation using a benchmark steroid dataset, J. Comput.-Aided Mol. Design 13, 271-296 (1999).
8. MATLAB Statistics Toolbox, Users Guide, The MATH-WORKS Inc. 24 Prime Park Way, Natick, MA 01760
9. TRIPOS Inc. 1699 S. Hanley Rd. St.Louis, MO 63144, USA
10. Clark, M, Cramer, R.D. III and Van Opdenbosch, Validation of the TRIPOS (5.2 Force Field, J. Comput. Chem. 10, 982-1012 (1989).
11. Frisch, M.J., Trucks, G.W., Head-Gordon, M., Gill, P.M.W., Wong, M.W., Foresman, J.B., Johnson, B.C., Schlegel, H.B., Robb, M.A., Replogle, E.S., Gomperts, R., Andres, J.L., Raghavachari, K., Binkley, J.S., Gonzalez, C., Martin, R.L., Fox, D.J., Defrees, D.J., Baker, J., Stewart, J.J.P., Pople, J.A., "Gaussian 92, Revision C," Gaussian Inc., 4415 Fifth Avenue,Pittsburgh, PA 15213.
12. Silverman, B.D. and Platt, D.E., Comparative Molecular Moment Analysis CoMMA: 3D-QSAR without Molecular Superposition, J. Med. Chem., 39, 2129-2140 (1996).
13. Joliffe, I.T., Principal Component Analysis, Springer Verlag 1986.
14. For a related discussion of the scaling of data, see, Jackson, J.E., A User's Guide to Principal Components, Chapter 3, John Wiley & Sons, 1991.
15. Comparative Molecular Moment Analysis (CoMMA) of the Anti-HIV-1 Activity of Twenty-four TIBO Derivatives. Web publication on the internet site http://www.research.ibm.com/ comma