作者
Marwen Naïm, Sathesh Bhat, Kathryn N Rankin, Sheldon Dennis, Shafinaz F Chowdhury, Imran Siddiqi, Piotr Drabik, Traian Sulea, Christopher I Bayly, Araz Jakalian, Enrico O Purisima
发表日期
2007/1/22
期刊
Journal of chemical information and modeling
卷号
47
期号
1
页码范围
122-133
出版商
American Chemical Society
简介
We present a binding free energy function that consists of force field terms supplemented by solvation terms. We used this function to calibrate the solvation model along with the binding interaction terms in a self-consistent manner. The motivation for this approach was that the solute dielectric-constant dependence of calculated hydration gas-to-water transfer free energies is markedly different from that of binding free energies (J. Comput. Chem. 2003, 24, 954). Hence, we sought to calibrate directly the solvation terms in the context of a binding calculation. The five parameters of the model were systematically scanned to best reproduce the absolute binding free energies for a set of 99 protein−ligand complexes. We obtained a mean unsigned error of 1.29 kcal/mol for the predicted absolute binding affinity in a parameter space that was fairly shallow near the optimum. The lowest errors were obtained with solute …
引用总数
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