title: Critical assessment of the automated AutoDock as a new docking tool for virtual screening.
abstract: A major problem in virtual screening concerns the accuracy of the binding free energy between a target protein and a putative ligand. Here we report an example supporting the outperformance of the AutoDock scoring function in virtual screening in comparison to the other popular docking programs. The original AutoDock program is in itself inefficient to be used in virtual screening because the grids of interaction energy have to be calculated for each putative ligand in chemical database. However, the automation of the AutoDock program with the potential grids defined in common for all putative ligands leads to more than twofold increase in the speed of virtual database screening. The utility of the automated AutoDock in virtual screening is further demonstrated by identifying the actual inhibitors of various target enzymes in chemical databases with accuracy higher than the other docking tools including DOCK and FlexX. These results exemplify the usefulness of the automated AutoDock as a new promising tool in structure-based virtual screening.
authors.affiliation: Department of Bioscience and Biotechnology, Sejong University, Seoul 143-747, Korea. hspark@sejong.ac.kr
authors.forename: Hwangseo
authors.initials: H
authors.lastname: Park
authors.forename: Jinuk
authors.initials: J
authors.lastname: Lee
authors.forename: Sangyoub
authors.initials: S
authors.lastname: Lee
mesh_terms: D015105:3',5'-Cyclic-AMP Phosphodiesterases / Q000737:chemistry; D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D054703:Cyclic Nucleotide Phosphodiesterases, Type 4; D051357:Cyclin-Dependent Kinase 2 / Q000737:chemistry; D051546:Cyclooxygenase 2 / Q000737:chemistry; D004791:Enzyme Inhibitors / Q000737:chemistry; D006801:Humans; D008024:Ligands; D011485:Protein Binding; D011487:Protein Conformation; D054562:Protein Tyrosine Phosphatase, Non-Receptor Type 1; D017027:Protein Tyrosine Phosphatases / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D004791:Enzyme Inhibitors; D008024:Ligands; D011506:Proteins; D051546:Cyclooxygenase 2; D051357:Cyclin-Dependent Kinase 2; C516607:PTPN1 protein, human; D054562:Protein Tyrosine Phosphatase, Non-Receptor Type 1; D017027:Protein Tyrosine Phosphatases; D015105:3',5'-Cyclic-AMP Phosphodiesterases; D054703:Cyclic Nucleotide Phosphodiesterases, Type 4