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Marcin Nowosielski, Marcin Hoffmann, Aneta Kuron, Malgorzata Korycka-Machala and Jaroslaw Dziadek The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics† Journal of Computational Chemistry 34

Version of Record online: 12 DEC 2012 | DOI: 10.1002/jcc.23192

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The ideal procedure for protein-ligand binding affinity prediction should be accurate, easily affordable in terms of computational time, and fully automated. Unfortunately, no method exists now that can satisfy all three requirements at the same time. A modified combined docking + molecular mechanics + quantum mechanical method is presented for accurate protein-ligand binding affinity prediction, together with the MM2QM tool for procedure automation. The procedure may be useful for finding analog inhibitors or improving drug candidates.

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