Computational protein-ligand docking and virtual drug screening with the AutoDock suite

Nat Protoc. 2016 May;11(5):905-19. doi: 10.1038/nprot.2016.051. Epub 2016 Apr 14.


Computational docking can be used to predict bound conformations and free energies of binding for small-molecule ligands to macromolecular targets. Docking is widely used for the study of biomolecular interactions and mechanisms, and it is applied to structure-based drug design. The methods are fast enough to allow virtual screening of ligand libraries containing tens of thousands of compounds. This protocol covers the docking and virtual screening methods provided by the AutoDock suite of programs, including a basic docking of a drug molecule with an anticancer target, a virtual screen of this target with a small ligand library, docking with selective receptor flexibility, active site prediction and docking with explicit hydration. The entire protocol will require ∼5 h.

Publication types

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

MeSH terms

  • Catalytic Domain
  • Drug Design
  • Drug Evaluation, Preclinical / methods*
  • Ligands
  • Molecular Docking Simulation*
  • Proteins / chemistry*
  • Proteins / metabolism
  • Software
  • Structure-Activity Relationship
  • User-Computer Interface


  • Ligands
  • Proteins