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Prediction of Ligand Binding Affinity by the Combination of Replica-Exchange Method and Double-Decoupling Method
Yuko Okamoto1,2,3,4, Hironori Kokubo5, Toshimasa Tanaka5
1Department of Physics, Graduate School of Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan.
Abstract:
A prediction method for ligand binding affinities to proteins is proposed. We first predict the structures of protein-ligand complex by the replica-exchange umbrella sampling or its extension. We then calculate ligand binding affinities based on these predicted ligand-protein bound structures by the double-decoupling method. As a test of the effectiveness of the proposed method, we applied it to the system of the oncoprotein MDM2 and a ligand. The value of the predicted binding affinity turned out to be in good agreement with that from experiments.
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