HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures.

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Abstract

Water molecules are integral to the structural stability of proteins and vital for facilitating molecular interactions. However, accurately predicting their precise position around protein structures remains a significant challenge, making it a vibrant research area. In this paper, we introduce HydraProt (deep Hydration of Proteins), a novel methodology for predicting precise positions of water molecule oxygen atoms around protein structures, leveraging two interconnected deep learning architectures: a 3D U-net and a Multi-Layer Perceptron (MLP). Our approach starts by introducing a coarse voxel-based representation of the protein, which allows for rapid sampling of candidate water positions via the 3D U-net. These water positions are then assessed by embedding the water-protein relationship in the Euclidean space by means of an MLP. Finally, a postprocessing step is applied to further refine the MLP predictions. HydraProt surpasses existing state-of-the-art approaches in terms of precision and recall and has been validated on large data sets of protein structures. Notably, our method offers rapid inference runtime and should constitute the method of choice for protein structure studies and drug discovery applications. Our pretrained models, data, and the source code required to reproduce these results are accessible at https://github.com/azamanos/HydraProt.