Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites

Dario Ghersi, Roberto Sanchez

Research output: Contribution to journalArticlepeer-review

85 Scopus citations


The use of predicted binding sites(binding sites calculated from the protein structure alone) is evaluated here as a tool to focus the docking of small molecule ligands into protein structures, simulating cases where the real binding sites are unknown. The resulting approach consists of a few independent docking runs carried out on small boxes, centered on the predicted binding sites, as opposed to one larger blind docking run that covers the complete protein structure. The focused and blind approaches were compared using a set of 77 known protein-ligand complexes and 19 ligand-free structures. The focused approach is shown to:(1) identify the correct binding site more frequently than blind docking;(2) produce more accurate docking poses for the ligand;(3) require less computational time. Additionally, the results show that very few real binding sites are missed in spite of focusing on only three predicted binding sites per target protein. Overall the results indicate that, by improving the sampling in regions that are likely to correspond to binding sites, the focused docking approach increases accuracy and efficiency of protein ligand docking for those cases where the ligand-binding site is unknown. This is especially relevant in applications such as reverse virtual screening and structure-based functional annotation of proteins.

Original languageEnglish (US)
Pages (from-to)417-424
Number of pages8
JournalProteins: Structure, Function and Bioinformatics
Issue number2
StatePublished - Feb 1 2009
Externally publishedYes


  • Astex diverse set
  • Autodock
  • Binding site discovery
  • Docking protocol
  • Reverse virtual screening

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology


Dive into the research topics of 'Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites'. Together they form a unique fingerprint.

Cite this