Dowser plus plus , a new method of hydrating protein structures

作者：Morozenko A^*; Stuchebrukhov A A^*

来源：Proteins: Structure, Function, and Genetics , 2016, 84(10): 1347-1357.

DOI：10.1002/prot.25081

• protein
• water
• hydration
• Dowser
• AutoDock
• WaterDock
• crystallography
• program
• cytochrome
• oxidase

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.

• 出版日期2016-10