Summary
A set of algorithms designed to enhance the display of protein binding cavities is presented. These algorithms, collectively entitled CAVITY SEARCH, allow the user to isolate and fully define the extent of a particular cavity. Solid modeling techniques are employed to produce a detailed cast of the active site region, which can then be color-coded to show electrostatic and steric interactions between the protein cavity and a bound ligand.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Marshall, G.R. and Naylor, C.B., In Ramsden, C.A. (Ed.), Comprehensive Medicinal Chemistry, Vol. 4, Pergamon Press, Oxford, 1990, pp. 431–458.
Blaney, J.M. and Hansch, C., In Ramsden, C.A. (Ed.), Comprehensive Medicinal Chemistry, Vol. 4, Pergamon Press, Oxford, 1990, pp. 459–496.
Connolly, M.L., Science, 221 (1983) 709.
Richards, F.M., Annu. Rev. Biophys. Bioeng., 6 (1977) 151.
Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S. and Weiner, P.K., J. Am. Chem. Soc., 106 (1984) 765.
Weiner, S.J., Kollman, P.A., Nguyen, D.T. and Case, D.A., J. Comput. Chem., 7 (1986) 230.
Fauchere, J.L., Quarendon, P. and Kaetterer, L., J. Mol. Graphics, 6 (1988) 203.
Furet, P., Sele, A. and Cohen, N.C., J. Mol. Graphics, 6 (1988) 182.
Fersht, A., Enzyme Structure and Mechanism, Freeman, New York, 1977.
Kuntz, I.D., Blaney, J.M., Oately, S.J., Langridge, R. and Ferrin, T.E., J. Mol. Biol., 161 (1982) 269.
Voorintholt, R., Kosters, M.T., Vegter, G., Vreind, G. and Hol, W.G.J., J. Mol. Graphics, 7 (1989) 243.
Casale, M.S. and Stanton, E.L., IEEE Computer Graphics and Applications, 5 (1985) 45.
Requicha, A.A.G. and Voelcker, H.B., IEEE Computer Graphics and Applications, 2 (1982) 9.
Requicha, A.A.G., IEEE Computer Graphics and Applications, 3 (1983) 25.
Hibert, M.F., Hoffmann, R., Miller, R.C. and Carr, A.A., J. Med. Chem., 33 (1990) 1594.
Sufrin, J.R., Dunn, D.A. and Marshall, G.R., Mol. Pharmacol., 19 (1981) 307.
Foley, J.D. and Van, Dam, A., Fundamentals of Interactive Computer Graphics, Addison-Wesley, Reading, MA, 1982.
Weiner, P.K., Landridge, C., Blaney, J.M., Schaefer, R. and Kollman, P.A., Proc. Natl. Acad. Sci. U.S.A., 79 (1982) 3754.
Miller, M., Schneider, J., Sathyanarayana, B.K., Toth, M.V., Marshall, G.R., Clawson, L., Selk, L., Kent, S.B.H. and Wlodawer, A., Science, 246 (1989) 1149.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Ho, C.M.W., Marshall, G.R. Cavity search: An algorithm for the isolation and display of cavity-like binding regions. J Computer-Aided Mol Des 4, 337–354 (1990). https://doi.org/10.1007/BF00117400
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00117400