Optimal water networks in protein cavities with GAsol and 3D-RISM

Fusani, Lucia and Wall, Ian and Palmer, David and Cortes, Alvaro (2018) Optimal water networks in protein cavities with GAsol and 3D-RISM. Bioinformatics. ISSN 1367-4803

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    Abstract

    Motivation: Water molecules in protein binding sites play essential roles in biological processes. The popular 3D-RISM prediction method can calculate the solvent density distribution within minutes, but is difficult to convert it into explicit water molecules. Results: We present GAsol, a tool that is capable of finding the network of water molecules that best fits a particular 3D-RISM density distribution in a fast and accurate manner and that outperforms other available tools by finding the globally optimal solution thanks to its genetic algorithm. Availability: https://github.com/accsc/GAsol. BSD 3-clauses license.

    ORCID iDs

    Fusani, Lucia, Wall, Ian, Palmer, David ORCID logoORCID: https://orcid.org/0000-0003-4356-9144 and Cortes, Alvaro;
    • Item type:Article
      ID code:62891
      Dates:
      Date
      Event
      15 January 2018
      Published
      15 January 2018
      Published Online
      8 January 2018
      Accepted
      Notes:This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record Fusani, L., Wall, I., Palmer, D., & Cortes, A. (2018). Optimal water networks in protein cavities with GAsol and 3D-RISM. Bioinformatics. is available online at: https://doi.org/10.1093/bioinformatics/bty024
      Keywords:3DRISM, protein-water interactions, placevent, drug discovery, computational chemistry, molecular docking, molecular integral equation theory, software, Chemistry, Biochemistry, Computational Mathematics, Molecular Biology
      Subjects:Science > Chemistry
      Department:Faculty of Science > Pure and Applied Chemistry
      Depositing user: Pure Administrator
      Date deposited:16 Jan 2018 11:51
      Last modified:05 May 2021 00:44
      Related URLs:
      URI:https://strathprints.strath.ac.uk/id/eprint/62891
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