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Protein Engineering, Vol. 7, No. 3. (01 March 1994), pp. 385-391, doi:10.1093/protein/7.3.385 Key: citeulike:4504895
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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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