PSNtools for standalone and web-based structure network analyses of conformational ensembles

Area of Science:

• Biophysics
• Structural Biology
• Bioinformatics

Background:

• Protein Structure Networks (PSNs) are powerful tools for understanding macromolecular function by representing interactions as graphs.
• Existing tools like Wordom and webPSN have limitations in analysis scope and post-processing capabilities.

Purpose of the Study:

• To introduce PSNtools, a novel standalone software for comprehensive PSN analysis.
• To provide enhanced capabilities for comparing and computing consensus networks from various structural data.
• To release an updated webPSN server for interactive analysis of PSN-MD data.

Main Methods:

• PSNtools calculates PSNs from single structures (using Elastic Network Model-Normal Mode Analysis - ENM-NMA) or molecular dynamics (MD) trajectories.
• The software facilitates network comparisons and consensus network computations on sets of homologous/analogous structures or conformational ensembles.
• An updated webPSN server supports interactive graphical analysis of PSN-MD outputs from PSNtools.

Main Results:

• PSNtools offers unique features for network comparison and consensus network generation.
• These new features allow inference of functional differences between states and identification of network signatures in related biomolecules.
• The integrated approach of PSNtools and the updated webPSN server provides a more complete workflow for PSN analysis.

Conclusions:

• PSNtools significantly advances the analysis of protein structure networks, offering novel comparative and consensus functionalities.
• The software and updated server empower researchers to explore macromolecular function and evolutionary relationships more effectively.
• PSNtools and webPSN are freely available, promoting wider accessibility to advanced PSN analysis techniques.