Software news and updates AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

Abstract

We describe the testing and release of AutoDock4 and the accompanying graphical user interface Auto- DockTools. 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 docking method and a modification of the flexible sidechain technique. © 2009 Wiley Periodicals, Inc.