Molecular docking simulations are now fast developing area of research. In this work we describe an effective procedure of preparation of the receptor-ligand complexes. The amino-acid residues involved in ligand binding were identified and described.
1.Kirkpatrick, S., Gelate, C.D., Jr. & Vecchi, M.P. (1983) Optimization by simulated annealing. Science 220, 671-680.
2.Cambridge Structural Database System. Cambridge Crystallographic Data Centre, Cambridge, U.K.
3.Pogozheva, I.D., Lomize, A.L. & Mosberg, H.I. (1998) Opioid receptor three-dimensional structures from distance geometry calculations with hydrogen bonding constraints. Biophys. J. 75, 612-634.
4.SYBYL v. 6.1 (1994) Tripos Inc., St. Louis, MO, U.S.A.
5.Palczewski, K., Kumasaka, T., Hori, T., Behnke, C.A., Motoshima, H., Fox, B.A., Le Trong, I., Teller, D.C., Okada, T., Stenkamp, R.E., Yamamoto, M. & Miyamoto, M. (2000) Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289, 739-745.
6.AMBER 5.0(2000) Pearlman, D.A., Case, D.A., Caldwell, J.W., Cheatham, III, T.E., Ross, W.S., Simmerling, C., Darden, T., Merz, K.M., Stanton, R.V., Cheng, A., Vincent, J.J., Crowley, M., Ferguson, D.M., Radmer, R., Seibel, G.L., Singh, U.C., Weiner, P. & Kollman, P.A., University of California, San Francisco.
7.GAMESS 98(1993) Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S, Jensen, J.H., Koseki, S., Matsunaga, N., Nguyen, K.A., Su, S., Windus, T.L., Dupuis, M. & Montgomery, J.A. J. Comput. Chem. 14, 1347-1363.
8.Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K. & Olson, A.J. (1998) Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J. Comput. Chem. 19, 1639-1662.
9.Solis, F.J. & Wets, R.J.-B. (1981) Minimization by random search techniques. Mathematical Operations Res. 6, 19-30.