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

Giulia Bianco, Stefano Forli, David S. Goodsell, Arthur J. Olson

Research output: Contribution to journalArticle

53 Scopus citations


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 (

Original languageEnglish (US)
Pages (from-to)295-301
Number of pages7
JournalProtein Science
Issue number1
StatePublished - Jan 1 2016


All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology


  • computational docking
  • computer-aided drug design
  • covalent inhibitors
  • ligand-protein interactions

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