Bioinformatics. 2024 Aug 17:btae516.
Krieger JM, Doljanin F, Bogetti AT, Zhang F, Manivarma T, Bahar I, Mikulska-Ruminska K.
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.
Supplementary information: Supplementary data are available at Bioinformatics online, and tutorials at http://www.bahargroup.org/prody.