RigFit: A new approach to superimposing ligand molecules

Abstract

If structural knowledge of a receptor under consideration is lacking, drug design approaches focus on similarity or dissimilarity analysis of putative ligands. In this context the mutual ligand superposition is of utmost importance. Methods that are rapid enough to facilitate interactive usage, that allow to process sets of conformers and that enable database screening are of special interest here. The ability to superpose molecular fragments instead of entire molecules has proven to be helpful too. The RigFit approach meets these requirements and has several additional advantages. In three distinct test applications, we evaluated how closely we can approximate the observed relative orientation for a set of known crystal structures, we employed RigFit as a fragment placement procedure, and we performed a fragment-based database screening. The run time of RigFit can be traded off against its accuracy. To be competitive in accuracy with another state-of-the-art alignment tool, with which we compare our method explicitly, computing times of about 6s per superposition on a common day workstation are required. If longer run times can be afforded the accuracy increases significantly. RigFit is part of the flexible superposition software FlexS which can be accessed on the WWW [http://cartan.gmd.de/FlexS].