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WatFinder: a ProDy tool for protein-water interactions.
Krieger, James M; Doljanin, Frane; Bogetti, Anthony T; Zhang, Feng; Manivarma, Thiliban; Bahar, Ivet; Mikulska-Ruminska, Karolina.
Afiliación
  • 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.
  • Bogetti AT; Department of Physics, Faculty of Science, University of Split, 21000, Split, Croatia.
  • Zhang F; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States.
  • Manivarma T; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States.
  • Bahar I; Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, 87100, Torun, Poland.
  • Mikulska-Ruminska K; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States.
Bioinformatics ; 40(8)2024 08 02.
Article en 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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Agua / Proteínas Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2024 Tipo del documento: Article País de afiliación: España Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Agua / Proteínas Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2024 Tipo del documento: Article País de afiliación: España Pais de publicación: Reino Unido