Effects of changing the bump limit on docking performance and time.

A & B) Differences for varying the bump limit at a match goal of 500 are shown here for one DUD-E target, Thyroid hormone receptor beta-1 (THB). This is one of the few cases where ligands and even some decoys find scores with a higher bump limit than they do with a lower bump limit in kcal/mol. C) The timings for this run and the mean over all 102 DUD-E targets is shown. The bump limit itself does not have a large effect on the time, but using a high bump limit instead of none roughly doubles the speed of docking.