Recipes for the selection of experimental protein conformations for virtual screening.

ABSTRACT: The use of multiple X-ray protein structures has been reported to be an efficient alternative for the representation of the binding pocket flexibility needed for accurate small molecules docking. However, the docking performance of the individual single conformations varies widely, and adding certain conformations to an ensemble is even counterproductive. Here we used a very large and diverse benchmark of 1068 X-ray protein conformations of 99 therapeutically relevant proteins, first, to compare the performance of the ensemble and single-conformation docking and, second, to find the properties of the best-performing conformers that can be used to select a smaller set of conformers for ensemble docking. The conformer selection has been validated through retrospective virtual screening exper

SUBMITTER: Rueda M 

PROVIDER: S-EPMC2811216 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature