computer modeling in molecular biology.pdf

4 Molecular Dynamics and Free Energy Calculations 99AcknowledgementsThe free energy simulations were carried out in close collaboration with M. Karplus(Harvard University) and B. Tidor (Whitehead Institute). M. P. is research associateat the National Fund for Scientific Research (Belgium). This work was supported inpart by the European Bridge Program (BIOT-CT91-0270).References[l] Goodfellow, J. M., Williams, M. A., Curr. Opin. Struct. Biol. 1992, 2, 211.[2] Gros, P., van Gunsteren, W. F., Hol, W. G. J., Science 1990, 249, 1149.[3] Torda, A. E., Scheek, R. M., van Gunsteren, W. F., J. Mol. Biol. 1990, 214, 223.[4] Nilges, M., Habazetti, J., Brunger, A. T., Holak, T. A., J. Mol. Biol. 1991, 219, 499.[5] Pearlman, D. A., Kollman, P. A., J. Mol. Biol. 1991, 220, 457.[6] Clore, G. M., Gronenborn, A. M., Protein Eng. 1987, I, 275.[7] Kaptein, R., Boelens, R., Scheek, R. M., van Gunsteren, W. F., Biochemistry 1988, 27,5389.[8] Kuryan, J., Osapay, K., Burley, S. K., Briinger, A. T., Hendrickson, W. A., Karplus, M.,Proteins 1991, 10, 340.[9] Chou, K.-C., Carlacci, I., Protein Eng. 1991, 4, 661.[lo] Wong, C. F., McCammon, A., J. Am. Chem. SOC. 1986, 108, 3380.[ll] Gao, J., Kuczera, K., Tidor, B., Karplus, M., Science 1989, 244, 1069.[12] Simonson, T., Briinger, A. T., Biochemistry 1992, 31, 8661.[13] Prkvost, M., Wodak, S. J., Tidor, B., Karplus, M., Proc. Natl. Acad. Sci. 1991, 88, 10880.[14] Kuczera, K., Gao, J., Tidor, B., Karplus, M., Proc. Natl. Acad. Sci. 1990, 87, 8481.[15] Mizushima, N., Spellmeyer, D., Hirono, S., Pearlman, D., Kollman, P. A., J. Biol. Chem.1991, 266, 11801.[16] Caldwel, J. W., Agard, D. A., Kollman, P. A., Proteins 1991, 10, 140.[17] Warshel, A., Sussman, F., Hwang, J.-K., J. Mol. Biol. 1988, 201, 139.[18] Yadav, A., Jackson, R. M., Holbrook, J. J., Warshel, A., J. Am. Chem. SOC. 1991, 113,4800.[19] Aqvist, J., Warshel, A., J. Mol. Biol. 1992, 224, 7.[20] Aqvist, J., J. Phys. Chem. 1991, 95, 4587.[21] Cecam Workshop, ‘Models for Protein Dynamics: Orsay, France, 1976.[22] Levitt, M., Sharon, R., Proc. Natl. Acad. Sci. USA 1988, 85, 7557.[23] Chandrasekhar, I., Clore, G. M., Szabo, A., Gronenborn, A. M., Brooks, B. R., .I Mol.Biol. 1992, 226, 239.[24] Lonchrich, R. J., Brooks, B. R., J. Mol. Biol. 1990, 215, 439.[25] Avbelj, F., Moult, J., Kitson, D. H., James, M. N. G., Hagler, A. T., Biochemistry 1990,29, 8658.[26] Brunne, R. M., Liepinsh, E., Otting, G., Wuthrich, K., van Gunsteren, W. F., J. Mol.Biol. 1993, 231, 1040.[27] Meiering, E. M., Bycroft, M., Fersht, A. R., Biochemistry 1991, 30, 11348.[28] Fersht, A. R., J. Mol. Biol. 1992, 224:3; this issue is entirely dedicated to the study ofstability and folding of barnase.