computer modeling in molecular biology.pdf

42 D. J. OsPuthorDe and J? K. C PaulMalikayil, J. A. and Harbeson, S. L., Int. J. Peptide Protein Res. 1992, 39, 497-505.Michel, A. G., Jeandenans, C., and Ananthanarayanan, V. S., J. Biomol. Str. Dyn. 1992, 10,281 -293.Mierke, D. F. and Kessler, H., J. Am. Chem. SOC. 1991, 113, 9466-9470.O’Connor, S. D., Smith, P. E., AlObeidi, F., and Pettitt, B. M., J. Med. Chem. 1992, 35,2870-2881.Ohno, Y., Segawa, M., Oshishi, H., Doi, M., Kitamura, K., Ishida, T., Inoue, M., andIwashita, T., Eur. J. Biochem. 1993, 212, 185-191.Palmer, A. G. and CAse, D. A., J. Am. Chem. SOC. 1992, 114, 9059-9067.Pardi, A., Zhang, X. L., Selsted, M. E., Skalicky, J. J., and Yip, P. F., Biochemistry 1992,31, 11357-11364.Paul, P. K. C., Dauber-Osguthorpe, P., Campbell, M. M., Brown, D. W., Kinsman, R. G.,Moss, C., and Osguthorpe, D. J., Biopolymers 1990, 29, 623.Paul, P. K. C., Dauber-Osguthorpe, P., Campbell, M. M., and Osguthorpe, D. J., Biochem.Biophys. Res. Comm. 1989, 165, 1051.Plinsky, A., Cooney, M. G., ToyPalmer, A., Osapay, G., and Goodman, M., J. Med. Chem.1992, 35, 4185-4194.Reilly, M. D. and Dunbar Jr, J. B., Biochem. Biophys. Res. Comm. 1991, 178, 570-577.Saudek, V., Hoflack, J., and Pelton, J. T., Znt. J. Peptide Protein Res. 1991, 37, 174-179.Saulitius, J., Mierke, D. F., Byk, G., Gilon, C., and Kessler, H., J. Am. Chem. SOC. 1992, 114,4818-4827.Saviano, M., Aida, M., and Corongiu, G., Biopolymers 1991, 31, 1017-1024.Schmidt, J. M., Ohlenschlager, O., Ruterjans, H., Grzonka, Z., Kojro, E., Pavo, I., andFahrenholz, F., Eur. J. Biochem. 1991, 201, 355-371.Sirnonson, T., and Brunger, A. T., Biochemistry 1992, 31, 8661-8614.Smith, P. E. and Dang, L. X., J. Am. Chem. SOC. 1991, 113, 67-73.Smith, P. E. and Pettitt, B. M., J. Am. Chem. SOC. 1991, 113, 6029-6037.Soman, K. V., Karimi, A., Case, D. A., Biopolymers 1991, 31, 1351-1361.Sukumar, M. and Higashijima, T., J. Biol. Chem. 1992, 21421-21424.TiradoRives, J. and Jorgensen, W. L., Biochemistry 1991, 30, 3864-3871.Tobias, D. J. and Brooks 111, C. L., Biochemistry 1991, 30, 6059-6070.Tobias, D. J., Mertz, J. E., and Brooks 111, C. L., Biochemistry 1991, 30, 6054-6058.Tobias, D. J., Sneddon, S. F., and Brooks 111, C. L., J. Mol. Biol. 1990, 216, 783-796.Ward, D. J., Chen, Y., Platt, E., and Robson, B., J. Theor. Biol. 1991, 148, 193-227.Wilkes, B. C. and Schiller, P. W., Znt. J Peptide Protein Res. 1992, 40, 249-254.Wolburn, U., Brunne, R. M., Harting, J., Holzemann, G., and Liebfritz, D., Int. .I. PeptideProtein Res. 1993, 41, 316-384.Zanotti, G., Majone, A., Rossi, F., Savino, M., Pedone, C., and Tancredi, T., Biopolymers1993, 33, 1083-1091.3.2 Energy Calculation MethodsMost peptide hormones have had some form of energetic study of their conformationalbehaviour. The first studies of peptide hormones used simple energy minimisationto determine local energy minimum conformations. Unfortunately, the flexiblenature of peptide hormones means that they have many structurally very dif-