WatFinder: a ProDy tool for protein-water interactions

被引：0

作者：

Krieger, James M. ^{[1
]}

Doljanin, Frane ^{[2
,3
]}

Bogetti, Anthony T. ^{[4
]}

Zhang, Feng ^{[4
]}

Manivarma, Thiliban ^{[2
]}

Bahar, Ivet ^{[4
,5
]}

Mikulska-Ruminska, Karolina ^{[2
]}

机构：

[1] Natl Ctr Biotechnol CNB CSIC, Dept Macromol Struct, Biocomp Unit, Calle Darwin 3,Campus UAM Cantoblanco, Madrid 28049, Spain

[2] Nicolaus Copernicus Univ Torun, Inst Phys, Fac Phys Astron & Informat, Grudziadzka 5 St, PL-87100 Torun, Poland

[3] Univ Split, Fac Sci, Dept Phys, Split 21000, Croatia

[4] SUNY Stony Brook, Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA

[5] SUNY Stony Brook, Renaissance Sch Med, Dept Biochem & Cell Biol, Stony Brook, NY 11794 USA

来源：

BIOINFORMATICS | 2024年 / 40卷 / 08期

基金：

美国国家卫生研究院; 欧盟地平线“2020”;

关键词：

MOLECULES;

D O I：

10.1093/bioinformatics/btae516

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页数：4

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