Abstract
This report describes the existence of statistical relationships among scores computed with the DOCK program for a library of small molecules and a panel of protein binding sites. Multivariate relationships are observed in docking scores computed for a constant set of ligands in different binding sites of proteins that are dissimilar in structure and function. The structural basis for the correlations found among scores is analyzed in terms of size, shape and charge characteristics of the binding sites considered. Interestingly, these results parallel a growing body of evidence demonstrating the promiscuous behavior of small molecules in their interactions with macromolecules that could have an impact in future efforts in drug design.
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References
Lengauer, T. and Rarey, M., Curr. Opin. Struct. Biol., 3 (1996) 402.
Gschwend, D.A., Good, A.C. and Kuntz, I.D., J. Mol. Recognit., 2 (1996) 175.
Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R. and Ferrin, T.E., J. Mol. Biol., 161 (1982) 269.
Kuntz, I.D., Science, 257 (1992) 1078.
Kuntz, I.D., Meng, E.C. and Shoichet, B.K., Acc. Chem. Res., 27 (1994) 117.
Shoichet, B.K., Bodian, D.L. and Kuntz, I.D., J. Comput. Chem., 13 (1992) 380.
Meng, E.C., Shoichet, B.K. and Kuntz, I.D., J. Comput. Chem., 13 (1992) 505.
Meng, E.C., Gschwend, D.A., Blaney, J.M. and Kuntz, I.D., Proteins, 17 (1993) 266.
Meng, E.C., Kuntz, I.D., Abraham, D.J. and Kellogg, G.E., J. Comput.-Aided Mol. Design, 8 (1994) 299.
Lorber, D.M. and Shoichet, B.K., Protein Sci., 4 (1988) 938.
Briem, H. and Kuntz, I.D., J. Med. Chem., 39 (1996) 3401.
Kauvar, M.L., Higgins, D.L., Villar, H.O., Sportsman, J.R., Engqvist-Goldstein, A., Bukar, R., Bauer, K.E., Dilley, H. and Rocke, D.M., Chem. Biol., 2 (1995) 107.
Connolly, M.L., Science, 221 (1983) 709.
Sussman, J.L., Harel, M., Frolow, F., Oefner, C., Goldman, A., Toker, L. and Silman, I., Protein Sci., 253 (1991) 872.
Banner, D.W. and Hadvary, P., J. Biol. Chem., 266 (1991) 20085.
Cooper, J., Quail, W., Frazao, C., Foundling, S.I., Blundell, T.L., Humblet, C., Lunney, E.A., Lowther, W.T. and Dunn, B.M., Biochemistry, 31 (1992) 8142.
Kamphuis, I.G., Kalk, K.H., Swarte, M.B. and Drenth, J., J. Mol. Biol., 179 (1984) 233.
Montfort, W.R., Perry, K.M., Fauman, E.B., Finer-Moore, J.S., Maley, G.F., Hardy, L., Maley, F. and Stroud, R.M., Biochemistry, 29 (1990) 6964.
Leslie, A.G., J. Mol. Biol., 213 (1990) 167.
Filman, D.J., Bolin, J.T., Matthews, D.A. and Kraut, J., J. Biol. Chem., 257 (1982) 13663.
Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., Jr. and Weiner, P., J. Am. Chem. Soc., 106 (1984) 765.
Gasteiger, J. and Marsili, M., Tetrahedron, 36 (1980) 3219.
Miller, A.J., Subset Selection in Regression. Monographs on Statistics and Applied Probability 40, Chapman and Hall, London, 1990.
Kuhn, L.A., Siani, M.A., Pique, M.E., Fisher, C.L., Getzoff, E.D. and Tainer, J.A., J. Mol. Biol., 228 (1992) 13.
Shoichet, B.K., Stroud, R.M., Santi, D.V., Kuntz, I.D. and Perry, K.M., Science, 259 (1993) 1445.
DesJarlais, R.L., Sheridan, R.P., Seibel, G.L., Dixon, J.S., Kuntz, I.D. and Venkataraghavan, R., J. Med. Chem., 31 (1988) 722.
Dixon, S.L. and Villar, H.O., J. Chem. Information Comput. Sci., 38 (1998) 1192.
Moodie, S.L., Mitchell, J.B. and Thornton, J.M., J. Mol. Biol., 263 (1996) 486.
La Bella, F.S., Biochem. Pharmacol., 42 (1991) S1.
Romesberg, F.E., Spiller, B., Schultz, P.G. and Stevens, R.C., Science, 279 (1998) 1929.
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Koehler, R.T., Villar, H.O. Statistical relationships among docking scores for different protein binding sites. J Comput Aided Mol Des 14, 23–37 (2000). https://doi.org/10.1023/A:1008136613726
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DOI: https://doi.org/10.1023/A:1008136613726