IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0226680.html
   My bibliography  Save this article

Improving graphs of cycles approach to structural similarity of molecules

Author

Listed:
  • Stefi Nouleho Ilemo
  • Dominique Barth
  • Olivier David
  • Franck Quessette
  • Marc-Antoine Weisser
  • Dimitri Watel

Abstract

This paper focuses on determining the structural similarity of two molecules, i.e., the similarity of the interconnection of all the elementary cycles in the corresponding molecular graphs. In this paper, we propose and analyze an algorithmic approach based on the resolution of the Maximum Common Edge Subgraph (MCES) problem with graphs representing the interaction of cycles molecules. Using the ChEBI database, we compare the effectiveness of this approach in terms of structural similarity and computation time with two calculations of similarity of molecular graphs, one based on the MCES, the other on the use of different fingerprints (Daylight, ECFP4, ECFP6, FCFP4, FCFP6) to measure Tanimoto coefficient. We also analyze the obtained structural similarity results for a selected subset of molecules.

Suggested Citation

  • Stefi Nouleho Ilemo & Dominique Barth & Olivier David & Franck Quessette & Marc-Antoine Weisser & Dimitri Watel, 2019. "Improving graphs of cycles approach to structural similarity of molecules," PLOS ONE, Public Library of Science, vol. 14(12), pages 1-25, December.
    • Handle: RePEc:plo:pone00:0226680
    DOI: 10.1371/journal.pone.0226680
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0226680
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0226680&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0226680?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0226680. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.