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.