RNAdvisor 2: A unified platform for RNA 3D model quality assessment using metrics, scoring functions, and meta-metrics

Abstract

RNA is a molecule that performs critical roles in cellular biology, with its function closely dependent on its three-dimensional conformation. Predicting and evaluating RNA 3D structures remains a significant challenge in the field. Although many metrics and scoring functions have been developed to assess structural quality, each offers a different perspective, and no single method has emerged as a definitive standard. To address this, we previously introduced RNAdvisor, a comprehensive and automated software platform to evaluate 3D RNA structures using a wide range of existing quality metrics and scoring functions. This work presents RNAdvisor2, an extended and improved version of the tool. RNAdvisor 2 introduces a web server designed to enhance accessibility and usability for the broader research community. This release includes new scoring functions and integrates the novel concepts of meta-metrics and meta-scoring functions, which unify diverse evaluation criteria into more robust indicators of RNA structure quality. Additionally, the command-line tool has been improved and optimized for greater stability and extensibility, supporting scalable and maintainable future development. The web server, tool and its source code are freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr.