title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.
abstract: We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique.
authors.affiliation: Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: Garrett M
authors.initials: GM
authors.lastname: Morris
authors.forename: Ruth
authors.initials: R
authors.lastname: Huey
authors.forename: William
authors.initials: W
authors.lastname: Lindstrom
authors.forename: Michel F
authors.initials: MF
authors.lastname: Sanner
authors.forename: Richard K
authors.initials: RK
authors.lastname: Belew
authors.forename: David S
authors.initials: DS
authors.lastname: Goodsell
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Olson
mesh_terms: D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011506:Proteins / Q000378:metabolism*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins