Blind docking of drug-sized compounds to proteins with up to a thousand residues

FEBS Lett. 2006 Feb 20;580(5):1447-50. doi: 10.1016/j.febslet.2006.01.074. Epub 2006 Jan 31.


Blind docking was introduced for the detection of possible binding sites and modes of peptide ligands by scanning the entire surface of protein targets. In the present study, the method is tested on a group of drug-sized compounds and proteins with up to a thousand amino acid residues. Both proteins from complex structures and ligand-free proteins were used as targets. Robustness, limitations and future perspectives of the method are discussed. It is concluded that blind docking can be used for unbiased mapping of the binding patterns of drug candidates.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Computer Simulation*
  • Drug Delivery Systems
  • Drug Design*
  • Ligands
  • Methods
  • Models, Molecular*
  • Protein Binding
  • Proteins / metabolism


  • Ligands
  • Proteins