GridSolvate: A Web Server for the Prediction of Biomolecular Hydration Properties

We
present a novel web server, named gridSolvate, dedicated to
the prediction of biomolecular hydration properties. Given a solute
in atomic representation, such as a protein or protein–ligand
complex, the server determines positions and excess chemical potential
of buried and first hydration shell water molecules. Calculations
are based on our semiexplicit hydration model that provides computational
efficiency close to implicit solvent approaches, yet captures a number
of physical effects unique to explicit solvent representation. The
model was introduced and validated before in the context of bulk hydration
of drug-like solutes and determination of protein hydration sites.
Current methodological developments merge those two avenues into a
single, easily accessible tool. Here, we focus on the server’s
ability to predict water distribution and affinity within protein–ligand
interfaces. We demonstrate that with possibly minimal user intervention
the server correctly predicts the locations of 77% of interface water
molecules in an external set of test structures. The server is freely
available at https://gsolvate.biomod.cent.uw.edu.pl.