Abstract
Significant progress has been achieved in computational methods to treat solvent effects in recent years. Among various techniques, the continuum solvent approach appears to be practically promising because it can be used to calculate reliable interaction and solvation energies in complex systems. A computational scanning mutagenesis method, one of such new approaches, has been recently developed. It combines the molecular mechanical and continuum solvent approaches and allows one to identify the `hotspots' in binding interfaces from a single trajectory of a wild type complex. Such techniques can be also used as a tool to optimize the interacting species for the binding, or as a ranking procedure in high throughput screening.
Similar content being viewed by others
References
Kollman, P.A., Chem. Rev., 93 (1993) 2395.
Smith, P. E. and Pettitt, B.M., J. Phys. Chem., 98 (1994) 9700.
Van Gunsteren, W.F., Luque, F.J., Timms, D. and Torda, A.E., Annu. Rev. Biophys. Biomol. Struct., 23 (1994) 847.
Tomasi, J. and Persico, M., Chem. Rev., 94 (1994) 2027.
Leach, A.R., Molecular Modelling: Principles and Applications, Addison Wesley Longman Ltd, Singapore, 1996, pp. 503–520.
Gao, J., Acc. Chem. Res., 29 (1996) 298.
Levy, R.M. and Gaillicchio, E., Annu. Rev. Phys. Chem., 49 (1998) 531.
Eisenberg, D. and McLachlan, A.D., Nature, 319 (1986) 199.
Born, M.Z., Phys., 1 (1920) 45.
Kirkwood, J.G., J. Chem. Phys., 2 (1934) 351.
Onsager, L., J. Am. Chem. Soc., 58 (1936) 1486.
Debye, P. and Hückel, E., Physik. Z., 24 (1923) 185.
Tanford, C. and Kirkwood, J.G., J. Am. Chem. Soc., 79 (1957) 5333.
Warwicker, J. and Watson, H.C., J. Mol. Biol., 157 (1982) 671.
Klapper, I., Hagstrom, R., Fine, R., Sharp, K. and Honig, B., Proteins, 1 (1986) 47.
Nicholls, A. and Honig, B., J. Comput. Chem., 12 (1990) 435.
Honig, B. and Nicholls, A., Science, 268 (1995) 1144.
Chen, J.L., Noodelman, L., Case, D.A. and Bashford, D., J. Phys. Chem., 98 (1994) 11059.
Madura, J.D., Briggs, J.M., Wade, R.C., Davis, M.E., Luty, B.A., Ilin, A., Antosiewicz, J., Gilson, M.K., Bagheri, B., Scott, L.R. and McCammon, J.A., Comput. Phys. Commun., 91 (1995) 57.
Sitkoff, D., Sharp, K.A. and Honig, B., J. Phys. Chem., 98 (1994) 1978.
Weiser, J., Shenkin, P.S. and Still, W.C., J. Comput. Chem., 20 (1999) 688.
You, T.J. and Bashford, D., Biophys. J., 65 (1995) 1721.
Wlodek, S.T., Antosiewicz, J. and McCammon. J.A., Protein Sci., 6 (1997) 373.
Beroza, P. and Case, D., J. Phys. Chem., 100 (1996) 20156.
Holst, M., Kozack, R.E., Saied, F. and Subramaniam, S., Proteins Struct. Funct. Genet., 18 (1994) 231.
Sharp, K.A., J. Comput. Chem., 12 (1991) 454.
Constanciel, R. and Contreras, R., Theor. Chim. Acta, 65 (1986) 1.
Still, W.C., Tempczyrk, A., Hawley, R.C. and Hendrickson, T., J. Am. Chem. Soc., 112 (1990) 6127.
Cramer, C.J. and Truhlar, D.G., J. Comput.-Aided Mol. Design, 6 (1992) 629.
Zhu, T.H., Li, J.B., Liotard, D.A., Cramer, C.J. and Truhlar, D.G., J. Chem. Phys., 110 (1999) 5503.
Zou, X., Sun, Y. and Kuntz, I.D., J. Am. Chem. Soc., 121 (1999) 8033.
Wong, M.W., Frisch, M.J. and Wiberg, K.B., J. Am. Chem. Soc., 113 (1991) 4776.
Rivail, J.L. and Rinaldi, D., Chem. Phys., 18 (1976) 233.
Miertuš, S. and Tomasi, J., Chem. Phys., 65 (1982) 329.
Klamt, A. and Schüürmann, G., J. Chem. Soc. Perkin Trans. II, 5 (1993) 799.
Gogonea, V. and Merz, K.M., J. Phys. Chem., A103 (1999) 5171.
Russell, S.T. and Warshel, A., J. Mol. Biol., 185 (1985) 389.
For example an additional 10-12 potential term.
Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.R., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P. and Kollman, P.A., AMBER4.1 (UCSF), University of California, San Francisco, CA, 1995.
Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M., J. Comput. Chem., 4 (1983) 187.
Jorgensen, W.L., BOSS3.6, Yale University, New Haven, CT, 1996.
Friesner, R.A. and Beachy, M.D., Curr. Opin. Struct. Biol., 8 (1998) 257.
Lyne, P.D., Hodoscek, M. and Karplus, M., J. Phys. Chem., 103 (1999) 3462.
Glennon, T.M. and Warshel, A., J. Am. Chem. Soc., 120 (1998) 12034.
Stanton, R.V., Peräkylä, M., Bakowies, D. and Kollman, P.A., J. Am. Chem. Soc., 120 (1998) 3448.
Srinivasan, J., Cheatham, T.E., Cieplak, P., Kollman, P.A. and Case, D.A., J. Am. Chem. Soc., 120 (1998) 9401.
Massova, I. and Kollman, P.A., J. Am. Chem. Soc., 121 (1999) 8133.
Chong, L.T., Duan, Y., Wang, L., Massova, I. and Kollman, P.A., Proc. Natl. Acad. Sci. USA, 96 (1999) 14330.
Darden, T., York, D. and Pedersen, L., J. Chem. Phys., 98 (1993) 10089.
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz Jr., K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A., J. Am. Chem. Soc., 117 (1995) 5179.
Karplus, M. and Kushick, J.N., Macromolecules, 14 (1981) 325.
Jayaram, B., Sprous, D. and Beveridge, D.L., J. Phys. Chem. B, 102 (1998) 9571.
Sanner, M.F., Olson, A.J. and Spehner, J.C., Biopolymers, 38 (1996) 305.
Böttger, A., Böttger, V., Garcia-Echeverria, C., Chè ne, P., Hochkeppel, H.K., Sampson, W., Ang, K., Howard, S.F., Picksley, S.M. and Lane, D.P., J. Mol. Biol., 269 (1997) 744.
Radmer, R.J. and Kollman, P.A., J. Comput.-Aided Mol. Design, 12 (1998) 215.
Bayly, C.I., Cieplak, P., Cornell, W.D. and Kollman, P.A., J. Phys. Chem., 97 (1993) 10269.
Clackson, T., Ultsch, M.H., Wells, J.A. and de Vos, A.M., J. Mol. Biol., 277 (1998) 1111.
Cunningham, B.C. and Wells, J.A., Science, 244 (1989) 1081.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Massova, I., Kollman, P.A. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspectives in Drug Discovery and Design 18, 113–135 (2000). https://doi.org/10.1023/A:1008763014207
Issue Date:
DOI: https://doi.org/10.1023/A:1008763014207