Biocomputing Unit, Department of Macromolecular Structure, National Center for Biotechnology (CNB-CSIC), Calle Darwin 3, Campus UAM Cantoblanco, 28049, Madrid, Spain.
Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, 87100, Torun, Poland.
Bioinformatics. 2024 Aug 2;40(8). doi: 10.1093/bioinformatics/btae516.
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.
ProDy is open-source and freely available under MIT License from https://github.com/ProDy/ProDy.
我们介绍了 WatFinder，这是一款用于识别和可视化与蛋白质稳定性、动力学和功能相关的蛋白质-水相互作用（水桥、水介导的相互作用或水通道、通量和簇）的工具。WatFinder 集成到了 ProDy 中，ProDy 是一个广泛用于基于结构预测蛋白质动力学的 Python API。WatFinder 提供了一套生成原始数据以及统计分析输出的功能。ProDy 框架便于全面自动化和有效地分析给定蛋白质的结构集合或在显式水中进行模拟的时变构象，这在补充材料中呈现的五个案例研究中得到了说明。
ProDy 是开源的，根据 MIT 许可证可在 https://github.com/ProDy/ProDy 上免费获取。
