Ribocentre-FoldBridge: a comprehensive database bridging RNA chemical probing data and 3D structures
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Updated: Nov 6, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Hao Sun1,2, Linyan Hu3,4, Xuemei Peng5
1Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International BioIsland, Guangzhou 510005 Guangdong, China.
Abstract:
RNA chemical probing generates nucleotide-resolved profiles in vitro and in cells, while X-ray crystallographic or cryo-electron microscopy models provide high-resolution structural models but remain comparatively low throughput. Aligning these experiments from different modalities may provide insights into RNA structure formation and molecular functions. Here, we present Ribocentre-FoldBridge (https://foldbridge.ribocentre.org/), an AI-assisted, curator-reviewed database linking curated chemical-probing profiles with experimentally determined 3D structures. This database catalogues 12 types of RNAs, linking 256 929 probing profiles across five experimental categories to 5321 structure-linked cases. It interactively visualizes the probing profiles that align with RNA secondary and tertiary structures at nucleotide resolution. We demonstrate probe-specific reactivity patterns across paired, unpaired, and solvent-accessible structural contexts. The database aims to provide a reproducible evidence layer for examining RNA structure-function relationships across heterogeneous experiments, and thus facilitate the development of new RNA structure or function prediction programs.
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