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

Lucia Fusani; Ian Wall; David Palmer; Alvaro Cortes

doi:10.1093/bioinformatics/bty024

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

Lucia Fusani, Ian Wall, David Palmer, Alvaro Cortes

Pure And Applied Chemistry

Research output: Contribution to journal › Article › peer-review

21 Citations (Scopus)

30 Downloads (Pure)

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.

Original language	English
Number of pages	2
Journal	Bioinformatics
Early online date	15 Jan 2018
DOIs	https://doi.org/10.1093/bioinformatics/bty024
Publication status	E-pub ahead of print - 15 Jan 2018

Keywords

3DRISM
protein-water interactions
placevent
drug discovery
computational chemistry
molecular docking
molecular integral equation theory
software

Access to Document

10.1093/bioinformatics/bty024

Fusani-etal-Bioinformatics-2018-Optimal-water-networks-in-protein-cavities-with-GAsolAccepted author manuscript, 958 KB

Cite this

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title = "Optimal water networks in protein cavities with GAsol and 3D-RISM",

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.",

keywords = "3DRISM, protein-water interactions, placevent, drug discovery, computational chemistry, molecular docking, molecular integral equation theory, software",

author = "Lucia Fusani and Ian Wall and David Palmer and Alvaro Cortes",

note = "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",

year = "2018",

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doi = "10.1093/bioinformatics/bty024",

language = "English",

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AU - Wall, Ian

AU - Palmer, David

AU - Cortes, Alvaro

N1 - 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

PY - 2018/1/15

Y1 - 2018/1/15

N2 - 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.

AB - 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.

KW - 3DRISM

KW - protein-water interactions

KW - placevent

KW - drug discovery

KW - computational chemistry

KW - molecular docking

KW - molecular integral equation theory

KW - software

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M3 - Article

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JO - Bioinformatics

JF - Bioinformatics

ER -

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

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

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David Palmer

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