AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

TLDR

The authors present the testing and release of AutoDock4 and its graphical user interface AutoDockTools. AutoDock4 introduces limited receptor flexibility and was evaluated through redocking of 188 ligand–protein complexes, cross‑docking of 87 HIV protease complexes with flexible sidechains, and analysis of covalently bound ligands using grid‑based docking and a modified side‑chain approach. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009.

Abstract

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. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009