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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Journal of Computational Chemistry · 2009 · Vol. 30(16) · pp. 2785–2791
Garrett M. Morris(Scripps Research Institute)Ruth Huey(Scripps Research Institute)William Lindstrom(Scripps Research Institute)Michel F. Sanner(Scripps Research Institute)Richard K. Belew(University of California, San Diego)David S. Goodsell(Scripps Research Institute)Arthur J. Olson✉(Scripps Research Institute)
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.
Computational Drug Discovery MethodsHIV/AIDS drug development and treatmentHIV Research and TreatmentDocking (animal)Searching the conformational space for dockingChemistryProtein–ligand dockingComputer scienceGridFlexibility (engineering)Covalent bondGraphical user interfaceCombinatorial chemistry
MeSH terms
LigandsModels, MolecularProtein BindingProteinsSoftware
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