AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

J Comput Chem. 2009 Dec;30(16):2785-91. doi: 10.1002/jcc.21256.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Ligands
  • Models, Molecular
  • Protein Binding
  • Proteins / metabolism*
  • Software*


  • Ligands
  • Proteins