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

Lucia Fusani, Ian Wall, David Palmer, Alvaro Cortes

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.
LanguageEnglish
Number of pages2
JournalBioinformatics
Early online date15 Jan 2018
DOIs
Publication statusE-pub ahead of print - 15 Jan 2018

Fingerprint

Cavity
Molecules
Proteins
Protein
Water
Biological Phenomena
Binding sites
Licensure
Protein Binding
Convert
Availability
Optimal Solution
Genetic algorithms
Binding Sites
Genetic Algorithm
Calculate
Prediction

Keywords

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

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.",
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Optimal water networks in protein cavities with GAsol and 3D-RISM. / Fusani, Lucia; Wall, Ian; Palmer, David; Cortes, Alvaro.

In: Bioinformatics, 15.01.2018.

Research output: Contribution to journalArticle

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T1 - Optimal water networks in protein cavities with GAsol and 3D-RISM

AU - Fusani, Lucia

AU - Wall, Ian

AU - Palmer, David

AU - Cortes, Alvaro

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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.

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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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