期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 79, 期 12, 页码 3400-3409出版社
WILEY
DOI: 10.1002/prot.23079
关键词
estimating pK(a) values; Poisson-Boltzmann; smooth dielectric boundary; staphylococcal nuclease
The results of two rounds of blind pK(a) predictions for ionizable residues in staphylococcal nuclease using OpenEye's legacy protein pK(a) prediction program based on the Zap Poisson-Boltzmann solver were submitted to the 2009 prediction challenge organized by the Protein pK(a) Cooperative and first round predictions were discussed at the corresponding June 2009 Telluride conference. To better understand these results, 21 additional sets of predictions were performed with the same program, varying the internal dielectric, reference pK(a), partial charge set, and dielectric boundary. The internal dielectric (epsilon(p)) and dielectric boundary were the two most important factors contributing to the quality of the predictions. Although the lowest overall errors were observed with a molecular dielectric boundary at epsilon(p) = 8, predictions using a smooth Gaussian dielectric boundary performed almost as well at lower epsilon(p) values because the Gaussian boundary implicitly accounts for a significant level of solvent penetration. Improved pK(a) predictions with the Gaussian boundary methodology will require better prediction and modeling of structural changes due to changes in ionization state, perhaps without resorting to the more exhaustive sampling of conformational states used by other recent continuum methods. Proteins 2011; 79:3400-3409. (C) 2011 Wiley-Liss, Inc.
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