ARNy Plotter: A Comprehensive Web Server for RNA Ensemble Structural Analysis and Visualization

Abstract Analyzing RNA structural ensembles, whether derived from molecular dynamics, enhanced sampling techniques, or experimental data, poses significant challenges due to the intrinsic flexibility and diverse conformational landscapes of RNA. We present ARNy Plotter, a web-based platform designed for comprehensive analysis and visualization of RNA structural ensembles. ARNy Plotter integrates multiple state-of-the-art methods into a unified, user-friendly environment, enabling intuitive examination of RMSD and eRMSD distributions, torsion-angle variability, dynamic secondary-structure patterns, contact-frequency networks, and multidimensional conformational landscapes. By leveraging MDAnalysis, Barnaba, and foRNA, the platform supports all major trajectory and ensemble formats while offering real-time 3D visualization via MolStar. Unlike existing tools that focus primarily on static structures or provide limited dynamic analysis, ARNy Plotter allows in-depth exploration of conformational transitions and population distributions within RNA ensembles, and facilitates result sharing without distributing full datasets. This platform addresses the growing need for accessible, comprehensive, and interactive tools for RNA structural biology. ARNy Plotter is freely available at https://arny-plotter.rpbs.univ-paris-diderot.fr/ , requires no installation or registration, and can also be run offline with a local webserver, including an API for automated figure generation.