AceDock: Virtual Screening And Docking

Screening large compound libraries


Screening allows for reducing the compounds which need to go to experimental testing. Our docking protocol, where we used KDEEP to re-score docked poses, won 2 blind sub-challenges of the D3R Grand Challenge 4. With our docking software, we can cover several relevant scenarios:

  • Free docking: No restrictions or prior knowledge is imposed in the docking exercise. Poses are re-scored with KDEEP.
  • Scaffold-hopping: Identify compounds in your library with great pharmacophoric overlap against a known binder.
  • Ensemble docking: We build an ensemble of conformations for your pocket to model protein flexibility.
  • Template docking: Use a known binder to guide the docking of a similar compound or series.
  • Constrained docking: Impose restrictions so certain moieties in the ligand (e.g. aromatic rings) are placed in the right spot.


  1. Protein preparation: The most suitable protonation states will be determined and hydrogens will be added.
  2. Mixed solvent molecular dynamics: The protonated target is simulated in a mixture of water and a fragment-size molecule, like benzene.
  3. Pocket profiling: Pharmacophores, structural waters and pocket ensembles are obtained from the simulations.
  4. Homolog search: Exhaustive search among public databases to find similar homologs with bound small molecules to further refine the pharmacophore.
  5. Molecular docking: The library of choice will be docked against the pocket ensemble and the obtained poses will be rescored after taking the pharmacophore and the waters into account.
  6. Ranking: The best compounds will be inspected and a short list of the most promising ones will be provided.


  • A PlayMolecule scene with binding mode predictions for the most promising compounds.
  • A ranking of compounds.
  • An extensive report summarizing the structural insights obtained.

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