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

ABSTRACT: 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.

SUBMITTER: Setny P 

PROVIDER: S-EPMC7768606 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature