We also benchmarked the speed of ligand docking in a number of real-life
virtual screening studies. In one study, a commercial library of 300,000 compounds
(STK library by Vitas-M Laboratory
was screened against a number of protein targets. Using a cluster of 16 computational
nodes (dual Xeon 5150 2.6 GHz) we were able to screen the entire
library in 12 to 24 hours depending on the protein target. The average time for docking
of a compound from the library for a particular protein is provided in the table above.
To estimate relative speed of docking calculations in different computing environments, the following table can be used as a guide: