Journal of Computer-Aided Molecular Design

, Volume 16, Issue 1, pp 59–71 | Cite as

Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases

  • John W. Raymond
  • Peter Willett


This paper reports an evaluation of both graph-based and fingerprint-based measures of structural similarity, when used for virtual screening of sets of 2D molecules drawn from the MDDR and ID Alert databases. The graph-based measures employ a new maximum common edge subgraph isomorphism algorithm, called RASCAL, with several similarity coefficients described previously for quantifying the similarity between pairs of graphs. The effectiveness of these graph-based searches is compared with that resulting from similarity searches using BCI, Daylight and Unity 2D fingerprints. Our results suggest that graph-based approaches provide an effective complement to existing fingerprint-based approaches to virtual screening.

fingerprint graph matching maximum common edge subgraph maximum overlapping set RASCAL similarity coefficient similarity searching virtual screening 


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Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • John W. Raymond
    • 1
  • Peter Willett
    • 2
  1. 1.Ann Arbor LaboratoriesPfizer Global Research and DevelopmentAnn ArborU.S.A
  2. 2.Krebs Institute for Biomolecular Research and Department of Information StudiesUniversity of SheffieldWestern Bank, SheffieldU.K

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