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Inverse frequency weighting of fragments for similarity-based virtual screening

Arif, S.M., Holliday, J.D. and Willett, P. (2010) Inverse frequency weighting of fragments for similarity-based virtual screening. Journal of Chemical Information and Modeling , 50 (8). pp. 1340-1349. ISSN 1549-9596

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This paper discusses the weighting of two-dimensional fingerprints for similarity-based virtual screening, specifically the use of weights that assign greatest importance to the substructural fragments that occur least frequently in the database that is being screened. Virtual screening experiments using the MDL Drug Data Report and World of Molecular Bioactivity databases show that the use of such inverse frequency weighting schemes can result, in some circumstances, in marked increases in screening effectiveness when compared with the use of conventional, unweighted fingerprints. Analysis of the characteristics of the various schemes demonstrates that such weights are best used to weight the fingerprint of the reference structure in a similarity search, with the database structures' fingerprints unweighted. However, the increases in performance resulting from such weights are only observed with structurally homogeneous sets of active molecules; when the actives arc diverse, the best results arc obtained using conventional, unweightecl fingerprints for both the reference structure and the database structures.

Item Type: Article
Institution: The University of Sheffield
Academic Units: The University of Sheffield > Faculty of Social Sciences (Sheffield) > Information School (Sheffield)
Depositing User: Miss Anthea Tucker
Date Deposited: 01 Jun 2011 09:34
Last Modified: 01 Jun 2011 09:34
Published Version: http://dx.doi.org/10.1021/ci1001235
Status: Published
Publisher: American Chemical Society
Identification Number: 10.1021/ci1001235
URI: http://eprints.whiterose.ac.uk/id/eprint/43049

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