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3D QSAR of Flexible Molecules Using Tensor Representation

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3D QSAR in Drug Design

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References

  1. Roberts, S.M. (Ed.), Molecular recognition: Chemical and biochemical problems II, Royal Society of Chemistry, Redwood Press, London, U.K., 1993.

    Google Scholar 

  2. Harisch, C., A quantitative approach to biochemical structure-activity relationships, Accts. Chem. Res., 2(1968) 232–239.

    Google Scholar 

  3. Hopfinger, AJ. and Tokurski, J.S., 3D-QSAR analysis, In Charifsom, P.S. (Ed.) Practical applications of computer-aided drug design, Marcel Dekker, New York, 1997.

    Google Scholar 

  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.

    Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  7. Cramer, R.D., Clark, R.D., Patterson, D.E. and Ferguson, A.M., Bioisosterism as a molecular diversity descriptor: Steric fields of single ‘topomeric’ confonners, J. Med. Chem., 39 (1996) 3060–3069.

    Article  CAS  Google Scholar 

  8. 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.

    CAS  Google Scholar 

  9. Crippen, G.M., Distance geometry approach to rationalizing binding data, J. Med. Chem., 22 (1979) 988–997.

    Article  CAS  Google Scholar 

  10. Doweyko, A.M., The hypothetical active site lattice: An approach to modeling active sites from data on inhibitor Molecules, Med.Chem., 31 (1988) 1396–1406.

    Article  CAS  Google Scholar 

  11. 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.

    Article  CAS  Google Scholar 

  12. Goodford, P.J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules, J. Med. Chem., 28 (1985) 849–856.

    Article  CAS  Google Scholar 

  13. Kubiny, H. (Ed.), 3D-QSAR in drug design: Theory, methods and applications, ESCOM, Leiden, The Netherlands, 1993.

    Google Scholar 

  14. 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.

    Article  CAS  Google Scholar 

  15. 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 dihydrofo/ate reductase: 3D-quantitutive 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.

    Article  CAS  Google Scholar 

  16. Tucker, L.R., Determination of parameters of a functional relation by factor analysis, Psychometrika, 23 (1958) 19–23.

    Google Scholar 

  17. Kroonenberg, P., Three mode principal component analysis, DSWO Press, Leiden, The Netherlands, 1983.

    Google Scholar 

  18. Apellof, C.J. and Davidson, E.R., Three dimensional rank annihilation for multicomponent determinations, Anal. Chim. Acta, 146 (1983) 9–14.

    Google Scholar 

  19. Sanchez, E. and Kowalski, B.R., Generalized rank annihilation factor analysis, Anal. Chem., 58 (1986) 496–499.

    Article  CAS  Google Scholar 

  20. 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.

    CAS  Google Scholar 

  21. 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): Aneutron diffraction study, J. Am. Chem. Soc., 98 (1976)2074–2081.

    Article  CAS  Google Scholar 

  22. Mabilia, M., Pearlstein, R.A. and Hopfinger, A.J., Molecular shape analysis and energetics-based intermolecular modeling of benzylpyrimidine dihydrofolatereductase inhibitors, Eur. J. Med. Chem.-Chim. Thera., 20 (1985) 163–174.

    CAS  Google Scholar 

  23. Dewar, M.J.S. and Thiel, W., Ground states of molecules: 38. The MNDO method, approximations and parameters, J. Am. Chem. Soc., 99 (1977) 4899–1906.

    CAS  Google Scholar 

  24. Hopfinger, A.J. and Pearlstein, R.A., Molecular mechanics force-field parameterization procedures, J. Comput. Chem., 5 (1985) 486–497.

    Google Scholar 

  25. 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.

    Google Scholar 

  26. Wold, S., Geladi, P., Eshensen, K. and Öhman, J., Multi-way principal comonents-and PLS-analysis, J. Chemornetrics, 1 (1987)41–56.

    CAS  Google Scholar 

  27. 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.

    Google Scholar 

  28. 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.

    Google Scholar 

  29. Lindgren, F., Geladi, P. and Wold, S., The kernel algorithm for PLS, J. Chemometrics, 7 (1993) 45–59.

    Article  CAS  Google Scholar 

  30. 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.

    Article  CAS  Google Scholar 

  31. Graham, A., Kronecker products and matrix calculus: With applications, Ellis Horwood, Chichester, U K., 1981.

    Google Scholar 

  32. Novotny, M.A., Matrix products with application to classical statistical mechanics, J. Math. Phys., 20 (1979)1146–1150.

    Article  Google Scholar 

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© 1998 Kluwer Academic Publishers

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Dunn, W.J., Hopfinger, A.J. (1998). 3D QSAR of Flexible Molecules Using Tensor Representation. In: Kubinyi, H., Folkers, G., Martin, Y.C. (eds) 3D QSAR in Drug Design. Three-Dimensional Quantitative Structure Activity Relationships, vol 3. Springer, Dordrecht. https://doi.org/10.1007/0-306-46858-1_11

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  • DOI: https://doi.org/10.1007/0-306-46858-1_11

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-0-7923-4791-0

  • Online ISBN: 978-0-306-46858-2

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