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Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

ARIEL: an openly accessible database of experimental RNA–ligand binding affinities paired with 3D structures

  • Mahmoud Omar Rasheed Zeyadah1
  • Amjad Jaber Alqahtani2
  • Sara Al Fliti2
  • Nahid Akhtar2
  • Suraj Sharma2
  • Andrea Petta3
  • Luigi Cavallo1
  • Romina Oliva4
  • Mohit Chawla1
4 affiliations
  1. 1Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 ,
  2. 2Department of Research and Innovation, STEMskills Research and Education Lab Pvt. Ltd , Faridabad 121002 ,
  3. 3Tagetik Software S.R.L , Lucca 55100 ,
  4. 4Department of Sciences and Technologies, University Parthenope of Naples , Centro Direzionale Isola C4, I-80143, Naples,
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Abstract

RNA is an increasingly attractive target for small-molecule therapeutics, yet the rational design and computational modelling of RNA-binding small molecules are constrained by the scarcity of experimentally measured binding affinities linked to 3D structures. Here we present ARIEL (Affinity Resource for Interactions of RNA and Ligands), an openly accessible, manually curated database that pairs experimentally determined dissociation constants (Kd) of RNA–ligand complexes with the corresponding experimental structures. We screened 6954 RNA-containing structures from the Protein Data Bank, extracted 2843 complexes with a small ligand, and manually curated the associated primary literature to retrieve the corresponding Kd values. This yielded a nonredundant dataset of 278 RNA–ligand complexes with experimental affinities, including 179 unique ligands bound to 171 different RNA targets, with Kd values spanning nine orders of magnitude (−log Kd 2.1–11.0). Each entry also provides the Kd measurement method and conditions, full literature provenance, ligand physicochemical descriptors, and binding-pocket annotations, with direct cross-links between structures, ligands and source publications. ARIEL will be maintained through regular, versioned releases; it is freely available at https://aocdweb.com/BioTools/ARIEL/.

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Cite

BibTeXRIS
BibTeX
@article{zeyadah2026ariel,
  title = {{ARIEL: an openly accessible database of experimental RNA–ligand binding affinities paired with 3D structures}},
  author = {Mahmoud Omar Rasheed Zeyadah and Amjad Jaber Alqahtani and Sara Al Fliti and Nahid Akhtar and Suraj Sharma and Andrea Petta and Luigi Cavallo and Romina Oliva and Mohit Chawla},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1080},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1080/9005080},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - ARIEL: an openly accessible database of experimental RNA–ligand binding affinities paired with 3D structures
AU  - Mahmoud Omar Rasheed Zeyadah
AU  - Amjad Jaber Alqahtani
AU  - Sara Al Fliti
AU  - Nahid Akhtar
AU  - Suraj Sharma
AU  - Andrea Petta
AU  - Luigi Cavallo
AU  - Romina Oliva
AU  - Mohit Chawla
PY  - 2026
DA  - 2026/10/30
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1080
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1080/9005080
AB  - RNA is an increasingly attractive target for small-molecule therapeutics, yet the rational design and computational modelling of RNA-binding small molecules are constrained by the scarcity of experimentally measured binding affinities linked to 3D structures. Here we present ARIEL (Affinity Resource for Interactions of RNA and Ligands), an openly accessible, manually curated database that pairs experimentally determined dissociation constants (Kd) of RNA–ligand complexes with the corresponding experimental structures. We screened 6954 RNA-containing structures from the Protein Data Bank, extracted 2843 complexes with a small ligand, and manually curated the associated primary literature to retrieve the corresponding Kd values. This yielded a nonredundant dataset of 278 RNA–ligand complexes with experimental affinities, including 179 unique ligands bound to 171 different RNA targets, with Kd values spanning nine orders of magnitude (−log Kd 2.1–11.0). Each entry also provides the Kd measurement method and conditions, full literature provenance, ligand physicochemical descriptors, and binding-pocket annotations, with direct cross-links between structures, ligands and source publications. ARIEL will be maintained through regular, versioned releases; it is freely available at https://aocdweb.com/BioTools/ARIEL/.
SN  - 0305-1048
SN  - 1362-4962
ER  -