Dowser++, a new method of hydrating protein structures

ABSTRACT 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. © 2016 Wiley Periodicals, Inc.