ARNy plotter: A comprehensive web server for RNA ensemble structural analysis and visualization

Area of Science:

• Structural Biology
• Computational Biology
• Bioinformatics

Background:

• RNA molecules exhibit significant flexibility and diverse conformational landscapes, posing challenges for structural analysis.
• Existing tools often focus on static structures or offer limited dynamic analysis capabilities.

Purpose of the Study:

• To present ARNy Plotter, a user-friendly web platform for comprehensive analysis and visualization of RNA structural ensembles.
• To provide an integrated environment for exploring RNA dynamics and conformational heterogeneity.

Main Methods:

• ARny Plotter integrates multiple analysis methods including RMSD/eRMSD distributions, torsion-angle variability, dynamic secondary structures, and contact networks.
• The platform leverages MDAnalysis, Barnaba, and foRNA for data processing and MolStar for real-time 3D visualization.
• Supports all major trajectory and ensemble formats, with options for offline use and an API for automated figure generation.

Main Results:

• Enables intuitive examination of various aspects of RNA structural ensembles, including conformational landscapes and population distributions.
• Facilitates in-depth exploration of conformational transitions and dynamic patterns within RNA structures.
• Allows for sharing of results without distributing large datasets.

Conclusions:

• ARny Plotter addresses the need for accessible, comprehensive, and interactive tools in RNA structural biology.
• The platform enhances the study of RNA dynamics and conformational ensembles.
• Freely available online and supports offline use, promoting wider adoption in the research community.