Variability in Docking Success Rates Due to Dataset Preparation C. R. Corbeil, C. I. Williams and P. Labute The MOE software with the newly developed GBVI/WSA dG scoring function is used throughout the study. For 80 % of the Astex targets, the MOE docker produces a top-scoring pose within 2 Å of the X-ray structure. For 91 % of the targets a pose within 2 Å of the X-ray structure is produced in the top 30 poses.
Scaffold Replacement in MOE S. Grimshaw A new application for performing scaffold replacements, fragment linking, and R-group optimization is presented. The application is applied to the discovery of novel p38 MAP kinase inhibitors, using the structures of a screening hit and the mature BIRB-796 inhibitor as starting points.
Training a Scoring Function for the Alignment of Small Molecules S. L. Chan and P. Labute A comprehensive data set of aligned ligands with highly similar binding pockets from the Protein Data Bank has been built. Based on this data set, a scoring function for recognizing good alignment poses for small molecules has been developed.
J Chem Inf Model, 2010, 50 (9), pp 1724-1735