gr Predictor: a Deep-Learning Model for Predicting the Hydration Structures around Proteins

Abstract

ABSTRACTAmong the factors affecting biological processes such as protein folding and ligand binding, hydration, which is represented by a three-dimensional water-site-distribution-function around the protein, is crucial. The typical methods for computing the distribution functions, including molecular dynamics simulations and the three-dimensional reference interaction site model (3D-RISM) theory, require a long computation time from hours to tens of hours. Here, we propose a deep-learning model rapidly estimating the distribution functions around proteins obtained by the 3D-RISM theory from the protein 3D structure. The distribution functions predicted using our deep-learning model are in good agreement with those obtained by the 3D-RISM theory. Particularly, the coefficient of determination between the distribution function obtained by the deep-learning model and that obtained using the 3D-RISM theory is approximately 0.98. Furthermore, using a graphics processing unit (GPU), the calculation by the deep learning model is completed in less than one minute, more than 2 orders of magnitude faster than the calculation time of 3D-RISM theory. Therefore, our deep learning model provides a practical and efficient way to calculate the three-dimensional water-site-distribution-functions. The program called “gr Predictor” is available under the GNU General Public License from https://github.com/YoshidomeGroup-Hydration/gr-predictor.Table of Contents graphic