WatFinder: a ProDy tool for protein-water interactions.

Autor:	Krieger JM; Biocomputing Unit, Department of Macromolecular Structure, National Center for Biotechnology (CNB-CSIC), Calle Darwin 3, Campus UAM Cantoblanco, 28049, Madrid, Spain., Doljanin F; Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, 87100, Torun, Poland.; Department of Physics, Faculty of Science, University of Split, 21000, Split, Croatia., Bogetti AT; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States., Zhang F; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States., Manivarma T; Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, 87100, Torun, Poland., Bahar I; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States.; Department of Biochemistry and Cell Biology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, United States., Mikulska-Ruminska K; Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, 87100, Torun, Poland.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2024 Aug 02; Vol. 40 (8).
DOI:	10.1093/bioinformatics/btae516
Abstrakt:	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. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
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