期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 6, 期 12, 页码 3850-3856出版社
AMER CHEMICAL SOC
DOI: 10.1021/ct100504h
关键词
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资金
- National Institutes of Health [GM32136]
- European Commission [FP7-PEOPLE-2008-4-1-IOF, 234796-PPIdesign]
Monte Carlo free energy perturbation (MC/FEP) calculations have been applied to compute the relative binding affinities of 17 congeneric pyridazo-pyrimidinone inhibitors of the protein p38 alpha MAP kinase. Overall correlation with experimental data was found to be modest when the complexes were hydrated using a traditional procedure with a stored solvent box. Significant improvements in accuracy were obtained when the MC/FEP calculations were repeated using initial solvent distributions optimized by the water placement algorithm JAWS. The results underscore the importance of accurate placement of water molecules in a ligand binding site for the reliable prediction of relative free energies of binding.
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