ArticleBriefings in bioinformatics2024
RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- Limits of deep-learning-based RNA prediction methods.Nucleic acids research · 2026Article
- Spectral Graph Features for Reference-free RNA 3D Quality Assessment.bioRxiv : the preprint server for biology · 2026Article
- The RNA-Puzzles Assessments of RNA-Only Targets in CASP16.Proteins · 2026Article
- RNAdvisor 2: A unified platform for RNA 3D model quality assessment using metrics, scoring functions, and meta-metrics.Scientific reports · 2025Article
- Has AlphaFold3 achieved success for RNA?Acta crystallographica. Section D, Structural biology · 2025Article
- RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction.Bioinformatics (Oxford, England) · 2024Article
- RNAtango: Analysing and comparing RNA 3D structures via torsional angles.PLoS computational biology · 2024Article
- The structure assessment web server: for proteins, complexes and more.Nucleic acids research · 2024Article
- State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.NAR genomics and bioinformatics · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
RNA is a complex macromolecule that plays central roles in the cell. While it is well known that its structure is directly related to its functions, understanding and predicting RNA structures is challenging. Assessing the real or predictive quality of a structure is also at stake with the complex 3D possible conformations of RNAs. Metrics have been developed to measure model quality while scoring functions aim at assigning quality to guide the discrimination of structures without a known and solved reference. Throughout the years, many metrics and scoring functions have been developed, and no unique assessment is used nowadays. Each developed assessment method has its specificity and might be complementary to understanding structure quality. Therefore, to evaluate RNA 3D structure predictions, it would be important to calculate different metrics and/or scoring functions. For this purpose, we developed RNAdvisor, a comprehensive automated software that integrates and enhances the accessibility of existing metrics and scoring functions. In this paper, we present our RNAdvisor tool, as well as state-of-the-art existing metrics, scoring functions and a set of benchmarks we conducted for evaluating them. Source code is freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.