期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 84, 期 10, 页码 1347-1357出版社
WILEY
DOI: 10.1002/prot.25081
关键词
protein; water; hydration; Dowser; AutoDock; WaterDock; crystallography; program; cytochrome; oxidase
资金
- NSF [PHY 0646273]
- NIH [GM054052]
A new method of hydrating protein structures, which we call Dowser++, is presented. The method is based on a semi-empirical modification of a popular program for protein hydration Dowser, and the usage of protocols AutoDock Vina, and WaterDock. The positions of water molecules predicted by Dowser++ were compared with experimental data for a set of 14 high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules, as well as for the D- and K-channels of cytochrome c oxidase, and the recent data on PSII. Comparison is also made with the predictions of the original Dowser, and its improved version, Dowser+, described in our previous publication. We also present a model for quantitative estimation of the quality of water molecules placement made by a program, which includes an assumption of possible false negative data from the crystallographic analysis. The comparison of predictions made by Dowser++, Dowser and Dowser+ demonstrates significant improvement of predictive power of the new method. Proteins 2016; 84:1347-1357. (c) 2016 Wiley Periodicals, Inc.
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