Flexible docking simulations: Scaled collective variable Monte Carlo minimization approach using Bezier splines, and comparison with a standard Monte Carlo algorithm

Abstract

An algorithm for docking a flexible ligand onto a flexible or rigid receptor, using the scaled-collective-variables Monte Carlo with energy minimization approach, is presented. Energy minimization is shown to be one of the best techniques for distinguishing between native- and nonnative-generated conformations. Incorporation of this technique into a Monte Carlo procedure enables one to distinguish the native conformation directly during the conformational search. It avoids the generation of a large number of ligand conformers for which more sophisticated energy evaluation tools would have had to be applied to identify the nativelike conformations. The efficiency of the Monte Carlo minimization was greatly improved by incorporating a new grid-based energy evaluation technique using Bezier splines for which the energy function, as well as all of its derivatives, can be deduced from the values at the grid points. Comparison between our ECEPP/3-based algorithm and the Monte Carlo algorithm presented elsewhere (Hart, T. N.; Read, R. J. Prot Struct Funct Genet 1992, 13, 206–222) has been made for docking NH2DPheProArgCOOH, the noncovalent analog of NH2DPheProArg chloromethylketone (PPACK), onto the active site of human α-thrombin. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 244–252, 1999