title: Variability in docking success rates due to dataset preparation.
abstract: The results of cognate docking with the prepared Astex dataset provided by the organizers of the "Docking and Scoring: A Review of Docking Programs" session at the 241st ACS national meeting are presented. 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. Docking failures, defined as cases where the top scoring pose is greater than 2 Å from the experimental structure, are shown to be largely due to the absence of bound waters in the source dataset, highlighting the need to include these and other crucial information in future standardized sets. Docking success is shown to depend heavily on data preparation. A "dataset preparation" error of 0.5 kcal/mol is shown to cause fluctuations of over 20 % in docking success rates.
authors.affiliation: Chemical Computing Group, Suite 910, 1010 Sherbrooke Street West, Montreal, QC, H3A 2R7, Canada. ccorbeil@chemcomp.com
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Corbeil
authors.forename: Christopher I
authors.initials: CI
authors.lastname: Williams
authors.forename: Paul
authors.initials: P
authors.lastname: Labute
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins