Summary
A new and promising development in the field of computer simulation of molecular systems is the socalled thermodynamic cycle integration technique, which combines well-known results from statistical thermodynamics with powerful computer simulation methods. The basic formulas, the development and the applications in the areas of drug design, protein engineering and conformational analysis of this elegant technique are discussed.
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Van Gunsteren, W.F. and Berendsen, H.J.C., Biochem. Soc. Trans., 10 (1982) 301–305.
Hermans, J. (Ed) Molecular Dynamics and Protein Structure, Polycrystal Book Service, P.O. Box 27, Western Springs. IL 60558, 1985.
Ciccotti, G. and Hoover, W.G. (Eds.) Proceedings of the International School of Physics ‘Enrico Fermi’, course 97, on Molecular Dynamics Simulation of Statistical-Mechanical Systems, North-Holland, Amsterdam, 1986.
McCammon, J.A. and Harvey, S.C., Dynamics of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, 1987.
Quirke, N. and Jacucci, G., Molec. Phys., 45 (1982) 823–838.
Berendsen, H.J.C., Postma, J.P.M. and van Gunsteren, W.F., In Hermans, J. (Ed) Molecular Dynamics and Protein Structure, Polycrystal Book Service, Western Springs, 1985, p. 43–46.
Frenkel, D., In Ciccotti, G. and Hoover, W.G. (Eds) Proceedings of the International School of Physics ‘Enrico Fermi’, course 97, North-Holland, Amsterdam, 1986, p. 151–188.
Mezei, M. and Beveridge, D.L., Ann. N.Y. Acad. Sci., 482 (1986) 1–23.
Kirkwood, J.G., J. Chem. Phys., 3 (1935) 300–313.
Zwanzig, R.W., J. Chem. Phys., 22 (1954) 1420–1426.
Torrie, G.M. and Vallcau, J.P., Chem. Phys. Letters. 28 (1974) 578–581.
Okazaki, S., Nakanishi, K., Touhara, H. and Adachi, Y., J. Chem. Phys., 71 (1979) 2421–2429.
Postma, J.P.M., Berendsen, H.J.C. and Haak, J.R., Faraday Symp. Chem. Soc. 17 (1982) 55–67.
Tembe, B.L. and McCammon, J.A., Comput. Chem., 8 (1984) 281–283.
Jorgensen, W.L. and Ravimohan, C., J. Chem. Phys., 83 (1985) 3050–3054.
Mruzik, M.R., Abraham, F.F. and Pound, G.M., J. Chem. Phys., 64 (1976) 481–491.
Berens, P.H., Mackay, D.H.J., White, G.M. and Wilson, K.R., J. Chem. Phys. 79 (1983) 2375–2389.
Mezei, M., Swaminathan, S. and Beveridge, D.L., J. Am. Chem. Soc., 100 (1978) 3255–3256.
Postma, J.P.M., Molecular Dynamics of H2O, thesis. University of Groningen, 1985.
Van Gunsteren, W.F. and Berendsen, H.J.C., In Stozowski, J. (Ed) Proceedings of the Symposium on Computational Methods in Chemical Design: Molecular Modelling and Graphics. Elmau. 1986. Oxford University Press, Oxford. 1987.
Straatsma, T.P., Berendsen, H.J.C. and Postma, J.P.M., J. Chem. Phys., 85 (1986) 6720–6727.
Lybrand, T.P., Gosh, I. and McCammon, J.A., J. Amer. Chem. Soc., 107 (1985) 7793–7794.
Bash, P.A., Singh, U.C., Langridge, R. and Kollman, P.A., Science (in press).
Lybrand, T.P., McCammon, J.A. and Wipff, G., Proc. Natl. Acad. Sci. U.S.A., 83 (1986) 833–835.
Wong, C.F. and McCammon, J.A., J. Amer. Chem. Soc. (in press).
Bash, P.A., Singh, U.C., Brown, F.K., Langridge, R. and Kollman, P.A., Science, 235 (1987) 574–576.
Wong, C.F. and McCammon, J.A., 1sr. J. Chem. (in press).
Bash, P.A., Singh. U.C., Langridge, R. and Kollman, P.A., Science (in press).
Cross, A.J., Chem. Phys. Letters. 128 (1986) 198–202.
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van Gunsteren, W.F., Berendsen, H.J.C. Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry. J Computer-Aided Mol Des 1, 171–176 (1987). https://doi.org/10.1007/BF01676960
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DOI: https://doi.org/10.1007/BF01676960