Covalent docking using autodock: Two-point attractor and flexible side chain methods

Protein Sci. 2016 Jan;25(1):295-301. doi: 10.1002/pro.2733. Epub 2015 Jul 7.


We describe two methods of automated covalent docking using Autodock4: the two-point attractor method and the flexible side chain method. Both methods were applied to a training set of 20 diverse protein-ligand covalent complexes, evaluating their reliability in predicting the crystallographic pose of the ligands. The flexible side chain method performed best, recovering the pose in 75% of cases, with failures for the largest inhibitors tested. Both methods are freely available at the AutoDock website (

Keywords: computational docking; computer-aided drug design; covalent inhibitors; ligand-protein interactions.

Publication types

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

MeSH terms

  • Automation*
  • Ligands
  • Molecular Docking Simulation*
  • Proteins / chemistry*


  • Ligands
  • Proteins