Abstract

Grid-based methods are widely used for evaluation of conformations in automated docking and other techniques of structure-based drug design. Traditional non-directional and directional methods for evaluating hydrogen bonds in these methods, however, yield improper interactions in cases with adjacent hydrogen bonds, such as those that mediate base pairing in nucleic acids. An improved method of calculating hydrogen bond potentials is reported here, which predicts the proper geometry for ligands that form multiple hydrogen bonds with receptors.

Keywords: hydrogen bond directionality, automated docking, grid-based energy evaluation