Dowser++, a new method of hydrating protein structures.
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.
Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California, 95616. amorozenko@ucdavis.edu.
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Morozenko
Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California, 95616. stuchebr@chem.ucdavis.edu.
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Stuchebrukhov
D000465:Algorithms; D002352:Carrier Proteins / Q000737:chemistry*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry*; D003576:Electron Transport Complex IV / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008074:Lipoproteins / Q000737:chemistry*; D062105:Molecular Docking Simulation; D009842:Oligopeptides / Q000737:chemistry; D012984:Software; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D002352:Carrier Proteins; D029968:Escherichia coli Proteins; D008074:Lipoproteins; D009842:Oligopeptides; C499290:OppA protein, E coli; D014867:Water; D003576:Electron Transport Complex IV; C120006:endodeoxyribonuclease PsiI; D015252:Deoxyribonucleases, Type II Site-Specific
AutoDock; Dowser; WaterDock; crystallography; cytochrome; hydration; oxidase; program; protein; water