Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems

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Abstract

We present a new molecular dynamics method using Tsallis effective potential for the flexible docking problems of streptavidin/biotin and protein kinase C/phorbol-13-acetate. With a full flexibility of the ligands and a partial flexibility of the receptor active sites included, the new MD scheme accelerates the docking process significantly, by way of infrequent q-jumping and q-relaxation procedures between a normal potential energy surface and its transformed one by the Tsallis scheme. In the transformation, only the nonbonding interaction terms of an empirical potential energy function were employed. It has been found that the current method can predict the correctly docked structures in quite an effective way. Current results strongly indicate that this new MD method can be a very promising strategy for flexible ligand/flexible receptor docking.

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