WatFinder: a ProDy tool for protein-water interactions.
Bioinformatics
; 40(8)2024 08 02.
Article
in En
| MEDLINE
| ID: mdl-39152994
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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Water
/
Proteins
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2024
Document type:
Article
Affiliation country:
Spain
Country of publication:
United kingdom