Simple Method for Locating Possible Ligand Binding Sites on Protein Surfaces

Abstract

A new, fast, and easy-to-implement method, van der Waals-fast Fourier transform (vdW-FFT), for locating possible binding sites on the surface of a protein was developed and tested on a set of 15 different enzyme-ligand complexes. The method scans the whole protein surface and possible ligand orientations 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, were used. The method has been shown to work accurately on the fine grid. On the coarse grid, the vdW-FFT method failed only on two complexes. The C program implementing the method and test set of proteins is available free on our web site: http://biocomp.anu.edu.au/∼aab.