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Dowser++, a new method of hydrating protein structures
Author(s) -
Morozenko A.,
Stuchebrukhov A. A.
Publication year - 2016
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25081
Subject(s) - molecule , chemistry , set (abstract data type) , computer science , biological system , biology , organic chemistry , programming language
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.