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.
Creators(s): |
Fusani, Lucia, Wall, Ian, Palmer, David ![]() | Item type: | Article |
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ID code: | 62891 |
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: | 21 Jan 2021 09:47 |
Related URLs: | |
URI: | https://strathprints.strath.ac.uk/id/eprint/62891 |
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