Application of a molecular dynamics simulation method with a generalized effective potential to the flexible molecular docking problems

We present a new molecular dynamics method using Tsallis effective potentia l for the flexible docking problems of streptavidin/biotin and protein kina se C/phorbol-13-acetate. With a full flexibility of the ligands and a parti al flexibility of the receptor active sites included, the new MD scheme acc elerates the docking process significantly, by way of infrequent q-jumping and q-relaxation procedures between a normal potential energy sur-face 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 correc tly docked structures in quite an effective way. Current results strongly i ndicate that this new MD method can be a very promising strategy for flexib le ligand/flexible receptor docking.