AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

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 side-chains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based clocking method and a modification of the flexible sidechain technique. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 2785-2791, 2009