3D OSAR of Flexible Molecules Using Tensor Representation

Perspectives in Drug Discovery and Design

Volumn 12--14, Issue , 1998, Pages 167-182

  Dunn III, William J ^a   Hopfinger, Antony J ^a,b  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b Chem21 Group Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0009992916     PISSN: 09282866     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (34)

1. Roberts, S.M. (Ed.), Molecular recognition: Chemical and biochemical problems II, Royal Society of Chemistry, Redwood Press, London, U.K., 1993.
2. Hansch, C., A quantitative approach to biochemical structure-activity relationships, Accts. Chem. Res., 2 (1968) 232-239.
3. Hopfinger, A.J. and Tokarski, J.S., 3D-QSAR analysis, In Charifsom, P.S. (Ed.) Practical applications of computer-aided drug design, Marcel Dekker, New York, 1997.
4. Eliel, E.L., Allinger, N.L., Angyal, S.J. and Morrison, G.A., Conformational analysis, The American Chemical Society, Washington, DC, 1981, p. 1.
5. Barakat, M.T. and Dean, P.M., Molecular structure matching by simulated annealing: II. An exploration of the evolution of configuration landscape problems, J. Computer-Aided Mol. Design, 4 (1990) 317-330.
6. Cramer III, R.D., Patterson, R.E. and Bunce, J.D., Comparative molecular field analysis (CoMFA): 1. The effect of shape on binding of steroids to carrier proteins, J. Am. Chem. Soc., 110 (1988) 5959-5967.
7. Tripos Associates, 1699 Hanley Road, St. Louis, MO 63144, U.S.A.
8. Cramer, R.D., Clark, R.D., Patterson, D.E. and Ferguson, A.M., Bioisosterism as a molecular diversity descriptor: Steric fields of single 'topomeric' conformers, J. Med. Chem., 39 (1996) 3060-3069.
9. Good, A.C., Peterson, S.J. and Richards, W.G., QSARs from similarity matrices: Technique validation and application in the comparison of different similarity evaluation methods, J. Med. Chem., 36 (1993) 2929-2937.
10. Crippen, G.M., Distance geometry approach to rationalizing binding data, J. Med. Chem., 22 (1979) 988-997.
11. Doweyko, A.M., The hypothetical active site lattice: An approach to modeling active sites from data on inhibitor Molecules, J. Med. Chem., 31 (1988) 1396-1406.
12. Walters, D.E. and Hinds, R.M., Genetically evolved receptor models: A computational approach to construction of receptor models, J. Med. Chem., 37 (1994) 2527-2536.
13. Goodford, P.J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules, J. Med. Chem., 28 (1985) 849-856.
14. CATALYST, Molecular Simulation, Inc., San Diego, CA, U.S.A.
15. Kubinyi, H. (Ed.), 3D-QSAR in drug design: Theory, methods and applications, ESCOM, Leiden, The Netherlands, 1993.
16. Hopfinger, A.J., Burke, B.J. and Dunn III, W.J., A generalized formalism for three-dimensional quantitative structure-activity relationship using tensor representation, J. Med. Chem., 37 (1994) 3768-3774.
17. Dunn III, W.J., Hopfinger, A.J.,Catana, C. and Duraiswami, C., Solution of the conformation and alignment tensors for the binding of trimethoprim and its analogs to dihydrofolate reductase: 3D-quantitative structure-activity relationships study using molecular shape analysis, 3-way partial least squares regression and 3-way factor analysis, J. Med. Chem., 39 (1996) 4825-4832.
18. Tucker, L.R., Determination of parameters of a functional relation by factor analysis, Psychometrika, 23 (1958) 19-23.
19. Kroonenberg, P., Three mode principal component analysis, DSWO Press, Leiden, The Netherlands, 1983.
20. Apellof, C.J. and Davidson, E.R., Three dimensional rank annihilation for multicomponent determinations, Anal. Chim. Acta, 146 (1983) 9-14.
21. Sanchez, E. and Kowalski, B.R., Generalized rank annihilation factor analysis, Anal. Chem., 58 (1986) 496-499.
22. Zeng, Y. and Hopke, P.K., The application of three-mode factor analysis (TMFA) to receptor modeling of scenes particle data, Atmosph. Environ., 26A (1992) 1701-1711.
23. Koetzle, T.F. and Williams, G.J.B., The crystal and molecular structure of the antifolate drug trimethoprim (2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidine): A neutron diffraction study, J. Am. Chem. Soc., 98 (1976) 2074-2081.
24. Mabilia, M., Pearlstein, R.A. and Hopfinger, A.J., Molecular shape analysis and energetics-based intermolecular modeling of benzylpyrimidine dihydrofolate reductase inhibitors, Eur. J. Med. Chem.-Chim. Thera., 20 (1985) 163-174.
25. Dewar, M.J.S. and Thiel, W., Ground states of molecules: 38. The MNDO method, approximations and parameters, J. Am. Chem. Soc., 99 (1977) 4899-4906.
26. Hopfinger, A.J. and Pearlstein, R.A., Molecular mechanics force-field parameterization procedures, J. Comput. Chem., 5 (1985) 486-497.
27. Lohmöller, J.B. and Wold, H., Three-mode path models with latent variables and partial least squares (PLS) parameter estimation, In Proceedings of the European Meeting of the Psychometric Society, University of Groningen, The Netherlands, 1980, p. 50.
28. Wold, S., Geladi, P., Esbensen, K. and Öhman, J., Multi-way principal comonents- and PLS-analysis, J. Chemometrics, 1 (1987) 41-56.
29. Glen, W.G., Dunn III, W.J. and Scott, D.R., Principal components analysis and partial least squares regression, Tetrahedron Comput. Method., 2 (1989) 349-376.
30. Glen, W.G., Sarker, M., Dunn III, W.J. and Scott, D.R., UNIPALS: Software for principal components analysis and partial least squares regression, Tetrahedron Comput. Method., 2 (1989) 377-396.
31. Lindgren, F., Geladi, P. and Wold, S., The kernel algorithm for PLS, J. Chemometrics, 7 (1993) 45-59.
32. Bush, B.L. and Nachbar Jr., R.B., Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA, J. Comput.-Aided Mol. Design, 7 (1993) 587-619.
33. Graham, A., Kronecker products and matrix calculus: With applications, Ellis Horwood, Chichester, U.K., 1981.
34. Novotny, M.A., Matrix products with application to classical statistical mechanics, J. Math. Phys., 20 (1979) 1146-1150.