The Use of Weighted 2D Fingerprints in Similarity-Based Virtual Screening

Shereena M. Arif, John D. Holliday, Peter Willett

    Research output: Chapter in Book/Report/Conference proceedingChapter

    3 Citations (Scopus)

    Abstract

    The fingerprints that are widely used for similarity-based virtual screening typically encode the presence or absence of fragments, without any indication as to their relative importance. This chapter discusses the use of weighted fingerprints, where each fragment is associated with a weight denoting its degree of importance in quantifying the degree of similarity between a reference structure and a database structure. Extensive studies using the World of Molecular Bioactivity and MDL Drug Data Report databases show that weighting fragments according to their frequency of occurrence within a molecule can increase the effectiveness of screening, but that this is not the case when fragments are weighted according to their frequency of occurrence within a database.

    Original languageEnglish
    Title of host publicationAdvances in Mathematical Chemistry and Applications: Revised Edition
    PublisherElsevier Inc.
    Pages92-112
    Number of pages21
    Volume1
    ISBN (Print)9781681081977, 9781681081984
    DOIs
    Publication statusPublished - 21 Jan 2016

    Fingerprint

    Screening
    Bioactivity
    Molecules
    Pharmaceutical Preparations

    Keywords

    • /MDL Drug Data Report/database
    • /World of Molecular Bioactivity/database
    • Chemoinformatics
    • ECFC4 fingerprint
    • Extended connectivity fingerprint counts fingerprint
    • Fingerprint
    • Fragment weighting scheme
    • Frequency weighting
    • IDF weighting
    • Information retrieval
    • Inverse frequency weighting
    • Ligand-based virtual screening
    • Similarity coefficient
    • Similarity searching
    • Similarity-based virtual screening
    • TF weighting
    • Virtual screening
    • Weighting scheme

    ASJC Scopus subject areas

    • Chemistry(all)

    Cite this

    Arif, S. M., Holliday, J. D., & Willett, P. (2016). The Use of Weighted 2D Fingerprints in Similarity-Based Virtual Screening. In Advances in Mathematical Chemistry and Applications: Revised Edition (Vol. 1, pp. 92-112). Elsevier Inc.. https://doi.org/10.1016/B978-1-68108-198-4.50005-9

    The Use of Weighted 2D Fingerprints in Similarity-Based Virtual Screening. / Arif, Shereena M.; Holliday, John D.; Willett, Peter.

    Advances in Mathematical Chemistry and Applications: Revised Edition. Vol. 1 Elsevier Inc., 2016. p. 92-112.

    Research output: Chapter in Book/Report/Conference proceedingChapter

    Arif, SM, Holliday, JD & Willett, P 2016, The Use of Weighted 2D Fingerprints in Similarity-Based Virtual Screening. in Advances in Mathematical Chemistry and Applications: Revised Edition. vol. 1, Elsevier Inc., pp. 92-112. https://doi.org/10.1016/B978-1-68108-198-4.50005-9
    Arif SM, Holliday JD, Willett P. The Use of Weighted 2D Fingerprints in Similarity-Based Virtual Screening. In Advances in Mathematical Chemistry and Applications: Revised Edition. Vol. 1. Elsevier Inc. 2016. p. 92-112 https://doi.org/10.1016/B978-1-68108-198-4.50005-9
    Arif, Shereena M. ; Holliday, John D. ; Willett, Peter. / The Use of Weighted 2D Fingerprints in Similarity-Based Virtual Screening. Advances in Mathematical Chemistry and Applications: Revised Edition. Vol. 1 Elsevier Inc., 2016. pp. 92-112
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