Simple method for locating possible ligand binding sites on protein surfaces

A new, fast, and easy-to-implement method, van der Waals-fast Fourier trans form (vdW-FFT), for locating possible binding sites on the surface of a pro tein was developed and tested on a set of 15 different enzyme-ligand comple xes. The method scans the whole protein surface and possible ligand orienta tions in order to find the best geometrical match, which corresponds to the minimum of the modified vdW energy. Two different grids, fine and coarse, and two sets of MM parameters, from the OPLS and AMBER-94 force fields, wer e used. The method has been shown to work accurately on the fine grid. On t he coarse grid, the vdW-FFT method failed only on two complexes. The C prog ram implementing the method and test set of proteins is available free on o ur web site: http://biocomp.anu.edu.au/ similar to aab. (C) 1999 John Wiley & Sons, Inc.