WatFinder: a ProDy tool for protein-water interactions.

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

SUBMITTER: Krieger JM 

PROVIDER: S-EPMC11349191 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature