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Protein Eng. 1994 Mar;7(3):385-91.

A new method for predicting binding affinity in computer-aided drug design.

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  • 1Department of Molecular Biology, Uppsala University, 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.

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