期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 7, 期 2, 页码 525-537出版社
AMER CHEMICAL SOC
DOI: 10.1021/ct100578z
关键词
-
资金
- Danish Council for Strategic Research through Program Commission on Strategic Growth Technologies [2106-07-0030]
- ERUDESP EU collaborative project
In this study, we have revised the rules and parameters for one of the most commonly used empirical pK(a) predictors, PROPKA, based on better physical description of the desolvation and dielectric response for the protein. We have introduced a new and consistent approach to interpolate the description between the previously distinct classifications into internal and surface residues, which otherwise is found to give rise to an erratic and discontinuous behavior. Since the goal of this study is to lay out the framework and validate the concept, it focuses on Asp and Glu residues where the protein pK(a) values and structures are assumed to be more reliable. The new and improved implementation is evaluated and discussed; it is found to agree better with experiment than the previous implementation (in parentheses): rmsd = 0.79 (0.91) for Asp and Glu, 0.75 (0.97) for Tyr, 0.65 (0.72) for Lys, and 1.00 (1.37) for His residues. The most significant advance, however, is in reducing the number of outliers and removing unreasonable sensitivity to small structural changes that arise from classifying residues as either internal or surface.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据