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


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.


Docking Enrichment Pose-prediction Virtual screening GOLD Scoring function 



Cambridge Crystallographic Data Centre


Protein Data Bank


Root mean square deviation


Virtual screening


Receiver operating characteristic


Area under curve


Directory of useful decoys



This work was performed using the Darwin Supercomputer of the University of Cambridge High Performance Computing Service (, provided by Dell Inc. using Strategic Research Infrastructure Funding from the Higher Education Funding Council for England. We also thank Dr Colin Groom for valuable comments regarding the manuscript.


  1. 1.
    Jones G, Willett GP, Glen RC (1995) J Mol Biol 245:43–53CrossRefGoogle Scholar
  2. 2.
    Jones G, Willett P, Glen RC, Leach AR, Taylor RJ (1997) Mol Biol 267:727–748CrossRefGoogle Scholar
  3. 3.
    Sousa SJ, Alexandrino PS, Ramos MJ (2006) PROTEINS 65:15–26CrossRefGoogle Scholar
  4. 4.
    Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) J Comput Aided Mol Des 11:425–445CrossRefGoogle Scholar
  5. 5.
    Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD (2003) PROTEINS 52:609–623CrossRefGoogle Scholar
  6. 6.
    Mooij WTM, Verdonk M (2005) PROTEINS 61:272–287CrossRefGoogle Scholar
  7. 7.
    Korb O, Stützle T, Exner TE (2009) J Chem Inf Model 49(1):84–96CrossRefGoogle Scholar
  8. 8.
    Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WTM, Mortensen PN, Murray CW (2007) J Med Chem 50:726–741CrossRefGoogle Scholar
  9. 9.
  10. 10.
    Hendlich M, Bergner A, Günther J, Klebe G (2003) J Mol Biol 326:607–620CrossRefGoogle Scholar
  11. 11.
    Verdonk ML, Chessari G, Cole JC, Hartshorn MJ, Murray CW, Nissink JWM, Taylor RD, Taylor R (2005) J Med Chem 48:6504–6515CrossRefGoogle Scholar
  12. 12.
    Huang N, Shoichet BK, Irwin JJ (2006) J Med Chem 49:6789–6801CrossRefGoogle Scholar
  13. 13.
    Good AC, Oprea TI (2008) J Comput Aided Mol Des 22:169–178CrossRefGoogle Scholar
  14. 14.
    Dönneke D, Schweintz A, Stürzebecher A, Steinmetzer P, Schuster M, Stürzebecher U, Nicklisch S, Stürzebecher J, Steinmetzer T (2007) Bioorg & Med Chem Lett 17:3322–3329Google Scholar
  15. 15.
    Bender A, Glen RC (2005) J Chem Inf Model 45(5):1369–1375Google Scholar
  16. 16.
    Verdonk M, Giangreco I, Hall R, Korb O, Mortensen P, Murray CW (2011) J Med Chem 54:5422–5431CrossRefGoogle Scholar
  17. 17.
    Sutherland SJ, Nandigam RK, Erikson JA, Vieth M (2007) J Chem Inf Model 47:2293–2302CrossRefGoogle Scholar
  18. 18.
    Verdonk ML, Mortenson PN, Hall RJ, Hartshorn MJ, Murray CW (2008) J Chem Inf Model 48:2214–2225CrossRefGoogle Scholar
  19. 19.
    Sherman W, Day T, Jacobson MP, Friesner RA, Farid R (2006) J Med Chem 49(20):534–553CrossRefGoogle Scholar
  20. 20.
    Jain AN (2009) J Comput Aided Mol Des 23:355–374CrossRefGoogle Scholar

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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