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- W2005647584 abstract "An efficient molecular simulation methodology has been developed to determine the positioning of water molecules in the binding site of a protein or protein−ligand complex. Occupancies and absolute binding free energies of water molecules are computed using a statistical thermodynamics approach. The methodology, referred to as Just Add Water Molecules (JAWS), features “θ-water” molecules that can appear and disappear on a binding-site grid. Key approximations render the technique far more efficient than conventional free energy simulations. Testing of JAWS on five diverse examples (neuraminidase, scytalone dehydratase, major urinary protein 1, β-lactoglobulin, and COX-2) demonstrates its accuracy in locating hydration sites in comparison to results from high-resolution crystal structures. Possible applications include aid in refinement of protein crystal structures, drug lead optimization, setup of docking calculations, and simulations of protein−ligand complexes." @default.
- W2005647584 created "2016-06-24" @default.
- W2005647584 creator A5041098529 @default.
- W2005647584 creator A5053850265 @default.
- W2005647584 creator A5080825811 @default.
- W2005647584 date "2009-09-15" @default.
- W2005647584 modified "2023-10-16" @default.
- W2005647584 title "Prediction of the Water Content in Protein Binding Sites" @default.
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- W2005647584 doi "https://doi.org/10.1021/jp9047456" @default.
- W2005647584 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2891159" @default.
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- W2005647584 hasPublicationYear "2009" @default.
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