Protein Engineering vol. 7 no. 3 pp. 385-391, 1994
© 1994 Oxford University Press
RESEARCH-ARTICLE |
A new method for predicting binding affinity in computer-aided drug design
Department of Molecular Biology, Uppsala University Biomedical Centre, Box 590, S-75124 Uppsala 1Symbicom AB, Glunten, S-75183 Uppsala Sweden
A new semi–empirical method for calculating free energies of binding from molecular dynamics (MD) simulations is presented. It is based on standard thermodynamic cycles and on a linear approximation of polar and non–polar free energy contributions from the corresponding MD averages. The method is tested on a set of endothiapepsin inhibitors and found to give accurate results both for absolute as well as relative free energies.
Keywords: binding free energies/drug design/endothiapepsin/inhibitor binding/molecular dynamics simulation
Received June 28, 1993; revised November 4, 1993; accepted November 16, 1993.
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