Comparative evaluation of eight docking tools for docking and virtual screening accuracy

Proteins. 2004 Nov 1;57(2):225-42. doi: 10.1002/prot.20149.


Eight docking programs (DOCK, FLEXX, FRED, GLIDE, GOLD, SLIDE, SURFLEX, and QXP) that can be used for either single-ligand docking or database screening have been compared for their propensity to recover the X-ray pose of 100 small-molecular-weight ligands, and for their capacity to discriminate known inhibitors of an enzyme (thymidine kinase) from randomly chosen "drug-like" molecules. Interestingly, both properties are found to be correlated, since the tools showing the best docking accuracy (GLIDE, GOLD, and SURFLEX) are also the most successful in ranking known inhibitors in a virtual screening experiment. Moreover, the current study pinpoints some physicochemical descriptors of either the ligand or its cognate protein-binding site that generally lead to docking/scoring inaccuracies.

Publication types

  • Comparative Study
  • Evaluation Study

MeSH terms

  • Computer Graphics / standards*
  • Crystallography, X-Ray
  • Databases, Protein / standards
  • Drug Design
  • Herpesvirus 1, Human / chemistry
  • Herpesvirus 1, Human / enzymology
  • Libraries, Digital / standards
  • Ligands
  • Protein Structure, Quaternary
  • Software / standards*
  • Thymidine Kinase / chemistry
  • User-Computer Interface
  • Viral Proteins / chemistry


  • Ligands
  • Viral Proteins
  • Thymidine Kinase