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

Lucia Fusani, Ian Wall, David Palmer, Alvaro Cortes

Research output: Contribution to journalArticle

6 Citations (Scopus)
9 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 languageEnglish
Number of pages2
JournalBioinformatics
Early online date15 Jan 2018
DOIs
Publication statusE-pub ahead of print - 15 Jan 2018

Keywords

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

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