Effect of ligand volume correction on PMF scoring

Recently, a knowledge-based scoring function has been introduced that estimates the protein-binding affinity based on the 3D structure of a protein–ligand complex (J Med Chem 1999, 42, 791). A ligand volume correction factor has been proposed and applied to filter out intraligand interactions in this simplified potential approach. Here we evaluate the effect of the ligand volume correction on the predictive power of the PMF scoring function. It is found that the effect of the ligand volume correction is significant on the derived potentials and large on the overall score. However, the effect of the ligand correction on the predictive power of the scoring function appears to be smaller. For a test set containing serine proteases the predictive power of the PMF scoring function does not change with the introduction of the volume correction. For a test set of metalloprotease complexes, the predictive power of the PMF scoring function improves only slightly when the volume correction is applied. For five test sets comprising a total of 225 diverse protein ligand complexes taken from the Brookhaven Protein Data Bank it is found, however, that the introduction of the ligand volume correction consistently improves the correlation between the PMF scores and the measured binding affinities. The effect of the correction factor on docking/scoring experiments is also analyzed using a test set of 61 biphenyl inhibitor-stromelysin complexes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 418–425, 2001