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 1367-4811 (https://doi.org/10.1093/bioinformatics/bty024)
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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: https://orcid.org/0000-0003-4356-9144 and Cortes, Alvaro;-
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Item type: Article ID code: 62891 Dates: DateEvent15 January 2018Published15 January 2018Published Online8 January 2018AcceptedNotes: 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 Subjects: Science > Chemistry Department: Faculty of Science > Pure and Applied Chemistry Depositing user: Pure Administrator Date deposited: 16 Jan 2018 11:51 Last modified: 11 Nov 2024 11:53 Related URLs: URI: https://strathprints.strath.ac.uk/id/eprint/62891