期刊
JOURNAL OF PHYSICAL CHEMISTRY B
卷 113, 期 40, 页码 13337-13346出版社
AMER CHEMICAL SOC
DOI: 10.1021/jp9047456
关键词
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资金
- National Institutes of Health [GM32136]
- National Foundation for Cancer Research
- European Commission [FP7-PEOPLE-2008-4-1-IOF, 234796-PPIdesign]
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 theta-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 oil five diverse examples (neuraminidase, scytalone dehydratase, major Urinary protein 1, beta-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.
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