Journal
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume 16, Issue 1, Pages 59-71Publisher
SPRINGER
DOI: 10.1023/A:1016387816342
Keywords
fingerprint; graph matching; maximum common edge subgraph; maximum overlapping set; RASCAL; similarity coefficient; similarity searching; virtual screening
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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.
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