WatFinder: a ProDy tool for protein–water interactions

• DOI: 10.1093/bioinformatics/btae516
• Publication Date: 2024-08-17T14:27:00Z
• Authors: James M Krieger; Frane Doljanin; Anthony T Bogetti; Feng Zhang; Thiliban Manivarma; Ivet Bahar; Karolina Mikulska...
• Keywords: Applications Note; 0303 health sciences; 03 medical and health sciences; Protein Conformation; Proteins; Water; Molecular Dynamics Simulation; Software

Abstract

Summary We introduce WatFinder, a tool designed to identify and visualize protein–water interactions (water bridges, water-mediated associations, or water channels, fluxes, and clusters) relevant to protein stability, dynamics, and function. WatFinder is integrated into ProDy, a Python API broadly used for structure-based prediction of protein dynamics. WatFinder provides a suite of functions for generating raw data as well as outputs from statistical analyses. The ProDy framework facilitates comprehensive automation and efficient analysis of the ensembles of structures resolved for a given protein or the time-evolved conformations from simulations in explicit water, as illustrated in five case studies presented in the Supplementary Material.

Availability and implementation ProDy is open-source and freely available under MIT License from https://github.com/ProDy/ProDy.