期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 43, 期 4, 页码 403-412出版社
WILEY
DOI: 10.1002/prot.1053
关键词
pK(a) calculations; hydrogen-bond network optimization; electrostatics; Poisson-Boltzmann equation; protein structure optimization; crystal artifacts
pK(a) calculation methods that are based on finite difference solutions to the Poisson-Boltzmann equation (FDPB) require that energy calculations be performed for a large number of different protonation states of the protein. Normally, the differences between these protonation states are modeled by changing the charges on a few atoms, sometimes the differences are modeled by adding or removing hydrogens, and in a few cases the positions of these hydrogens are optimized locally. We present an FDPB-based pK(a) calculation method in which the hydrogen-bond network is globally optimized for every single protonation state used. This global optimization gives a significant improvement in the accuracy of calculated pK(a) values, especially for buried residues. It is also shown that large errors in calculated pK(a) values are often due to structural artifacts induced by crystal packing. Optimization of the force fields and parameters used in pK(a) calculations should therefore be performed with X-ray structures that are corrected for crystal artifacts. Proteins 2001;43:403-412. (C) 2001 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