Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results

  • Robert P. Sheridan
  • Georgia B. McGaughey
  • Wendy D. Cornell
Article

Abstract

As an extension to a previous published study (McGaughey et al., J Chem Inf Model 47:1504–1519, 2007) comparing 2D and 3D similarity methods to docking, we apply a subset of those virtual screening methods (TOPOSIM, SQW, ROCS-color, and Glide) to a set of protein/ligand pairs where the protein is the target for docking and the cocrystallized ligand is the target for the similarity methods. Each protein is represented by a maximum of five crystal structures. We search a diverse subset of the MDDR as well as a diverse small subset of the MCIDB, Merck’s proprietary database. It is seen that the relative effectiveness of virtual screening methods, as measured by the enrichment factor, is highly dependent on the particular crystal structure or ligand, and on the database being searched. 2D similarity methods appear very good for the MDDR, but poor for the MCIDB. However, ROCS-color (a 3D similarity method) does well for both databases.

Keywords

2D similarity 3D similarity Docking BEDROC ROC Glide ROCS SQ SQW TOPOSIM 

Notes

Acknowledgement

The authors thank Christopher Bayly for useful discussions.

Supplementary material

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Robert P. Sheridan
    • 1
  • Georgia B. McGaughey
    • 2
  • Wendy D. Cornell
    • 1
  1. 1.Molecular Systems DepartmentMerck Research LaboratoriesRahwayUSA
  2. 2.Molecular Systems DepartmentMerck Research LaboratoriesWest PointUSA

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