Journal of Computer-Aided Molecular Design

, Volume 26, Issue 6, pp 737–748 | Cite as

Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test

  • John W. Liebeschuetz
  • Jason C. Cole
  • Oliver Korb
Article

Abstract

The performance of all four GOLD scoring functions has been evaluated for pose prediction and virtual screening under the standardized conditions of the comparative docking and scoring experiment reported in this Edition. Excellent pose prediction and good virtual screening performance was demonstrated using unmodified protein models and default parameter settings. The best performing scoring function for both pose prediction and virtual screening was demonstrated to be the recently introduced scoring function ChemPLP. We conclude that existing docking programs already perform close to optimally in the cognate pose prediction experiments currently carried out and that more stringent pose prediction tests should be used in the future. These should employ cross-docking sets. Evaluation of virtual screening performance remains problematic and much remains to be done to improve the usefulness of publically available active and decoy sets for virtual screening. Finally we suggest that, for certain target/scoring function combinations, good enrichment may sometimes be a consequence of 2D property recognition rather than a modelling of the correct 3D interactions.

Keywords

Docking Enrichment Pose-prediction Virtual screening GOLD Scoring function 

Abbreviations

CCDC

Cambridge Crystallographic Data Centre

PDB

Protein Data Bank

RMSD

Root mean square deviation

VS

Virtual screening

ROC

Receiver operating characteristic

AUC

Area under curve

DUD

Directory of useful decoys

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • John W. Liebeschuetz
    • 1
  • Jason C. Cole
    • 1
  • Oliver Korb
    • 1
  1. 1.Cambridge Crystallographic Data CentreCambridgeUK

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