Summary: Flexible Protein­Ligand Docking by Global Energy
Optimization in Internal Coordinates
Maxim Totrov and Ruben Abagyan*
The Skirball Institute of Biomolecular Medicine, Biochemistry Department of New York University Medical College,
New York, New York
ABSTRACT Eight protein­ligand com-
plexes were simulated by using global optimiza-
tion of a complex energy function, including
solvation, surface tension, and side-chain en-
tropy in the internal coordinate space of the
flexible ligand and the receptor side chains
[Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235:
983­1002, 1994]. The procedure uses two types
of efficient random moves, a pseudobrownian
positional move [Abagyan, R.A., Totrov, M.M.,
Kuznetsov, D.A. J. Comp. Chem. 15:488­506,
1994] and a Biased-Probability multitorsion move
[Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235:
983­1002, 1994], each accompanied by full local
energy minimization. The best docking solu-

Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego

Collections: Biology and Medicine