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WatFinder: a ProDy tool for protein-water interactions
James M Krieger1, Frane Doljanin2,3, Anthony T Bogetti4
1Biocomputing Unit, Department of Macromolecular Structure, National Center for Biotechnology (CNB-CSIC), Calle Darwin 3, Campus UAM Cantoblanco, 28049, Madrid, Spain.
Bioinformatics (Oxford, England)
|August 17, 2024
Summary
WatFinder is a new tool for visualizing protein-water interactions, crucial for protein stability and function. Integrated into ProDy, it aids in analyzing protein dynamics from structural data.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Protein-water interactions significantly influence protein stability, dynamics, and function.
- Understanding these interactions is key to deciphering protein behavior and mechanisms.
- Existing tools may lack comprehensive capabilities for analyzing diverse protein-water networks.
Purpose of the Study:
- To introduce WatFinder, a novel computational tool for identifying and visualizing protein-water interactions.
- To integrate WatFinder into the ProDy Python API for enhanced usability and analysis.
- To provide functions for generating raw data and statistical analyses of water-mediated phenomena.
Main Methods:
- Development of WatFinder as a Python-based tool.
- Integration of WatFinder within the ProDy framework for structure-based dynamics prediction.
- Utilizing ProDy for automated analysis of structural ensembles and simulation trajectories in explicit water.
Main Results:
- WatFinder identifies various protein-water interactions, including water bridges, associations, channels, fluxes, and clusters.
- The tool generates raw data and statistical analysis outputs.
- Demonstrated utility through five case studies in the Supplementary Material, showcasing analysis of protein ensembles and simulations.
Conclusions:
- WatFinder offers a comprehensive solution for studying protein-water interactions.
- Its integration with ProDy facilitates efficient and automated analysis of protein dynamics and stability.
- The tool is valuable for researchers investigating the role of water in protein structure and function.
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