Optimal water networks in protein cavities with GAsol and 3D-RISM.
basic_science · Level V
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- Record sourced from PubMed, PMID 29346514.
- Also identified by DOI 10.1093/bioinformatics/bty024.
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Abstract
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. 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. https://github.com/accsc/GAsol. BSD 3-clauses license. alvaro.x.cortes@gsk.com. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Computational Biology
- Models, Molecular
- Proteins
- Software
- Water