Skip to content
DraconiticResearch
Search Sources API
190,839 studies31 sourcesUpdated just now
Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

Ribocentre-FoldBridge: a comprehensive database bridging RNA chemical probing data and 3D structures

  • Hao Sun1,2
  • Linyan Hu3,4
  • Xuemei Peng5
  • Wei Zhang1,6
  • Jiajun Lin1,6
  • Jingyi Huang7
  • Cheng Zhang4
  • Lin Huang5
  • Zhichao Miao1,3,8
8 affiliations
  1. 1Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International BioIsland, Guangzhou 510005 Guangdong ,
  2. 2School of Life Sciences, Sun Yat-sen University No. 135 , Xingang Xi Road, Guangzhou 510275 Guangdong ,
  3. 3Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology and Perioperative medicine, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University , Shanghai 200434 ,
  4. 4Bioscience and Biomedical Engineering Thrust, The Hong Kong University of Science and Technology (Guangzhou) , Duxue Road, Nansha District, Guangzhou 511458 Guangdong ,
  5. 5Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou 510120 ,
  6. 6School of Life Science and Technology, ShanghaiTech University , Shanghai 201210 ,
  7. 7School of Mechanical & Automotive Engineering, South China University of Technology , Guangzhou 510641 ,
  8. 8GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University , Guangzhou 511436 Guangdong ,
Open at sourcePDFDOICite

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.

Related

  1. MiRNA Atlas: A Literature-Derived Database of MicroRNAs Bridging Osteoarthritis and Appendage Regeneration
    A. T. Parker, V. B. Kraus
    bioRxivPreprintCC BY-NC-NDFull textMolecular biology & gene regulationbioRxiv
  2. STRAND: a comprehensive subcellular-resolved spatial transcriptome RNA architecture and navigation database
    Zhaoxu Wu, Yuying Huo, Wenqian Xu +2
    Nucleic Acids ResearchPeer-reviewedCC BY-NC 4.0Full textMolecular biology & gene regulationCrossref
  3. OrganiZymeDB: a comprehensive database of enzyme stability and function in the presence of organic solvents
    Romain Debruyne, Fabrizio Pucci
    Nucleic Acids ResearchPeer-reviewedCC BY-NC 4.0Full textMolecular biology & gene regulationCrossref
  4. MultiTargetDB: a comprehensive database of multitarget ligands for polypharmacology research and drug discovery
    Jinmei Pan, Haoyu Lin, Jintao Zhu +8
    Nucleic Acids ResearchPeer-reviewedCC BY-NC 4.0Full textMolecular biology & gene regulationCrossref
  5. ARIEL: an openly accessible database of experimental RNA–ligand binding affinities paired with 3D structures
    Mahmoud Omar Rasheed Zeyadah, Amjad Jaber Alqahtani, Sara Al Fliti +6
    Nucleic Acids ResearchPeer-reviewedCC BY-NC 4.0Full textMolecular biology & gene regulationCrossref

Cite

BibTeXRIS
BibTeX
@article{sun2026ribocentrefoldbridge,
  title = {{Ribocentre-FoldBridge: a comprehensive database bridging RNA chemical probing data and 3D structures}},
  author = {Hao Sun and Linyan Hu and Xuemei Peng and Wei Zhang and Jiajun Lin and Jingyi Huang and Cheng Zhang and Lin Huang and Zhichao Miao},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = nov,
  doi = {10.1093/nar/gkag1096},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1096/9013045},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - Ribocentre-FoldBridge: a comprehensive database bridging RNA chemical probing data and 3D structures
AU  - Hao Sun
AU  - Linyan Hu
AU  - Xuemei Peng
AU  - Wei Zhang
AU  - Jiajun Lin
AU  - Jingyi Huang
AU  - Cheng Zhang
AU  - Lin Huang
AU  - Zhichao Miao
PY  - 2026
DA  - 2026/11/05
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1096
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1096/9013045
AB  - 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.
SN  - 0305-1048
SN  - 1362-4962
ER  -