Ys. Pak et Sm. Wang, Application of a molecular dynamics simulation method with a generalized effective potential to the flexible molecular docking problems, J PHYS CH B, 104(2), 2000, pp. 354-359
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.