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

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ID: 337897
2026
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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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openalex_W7224747635 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Mahmoud Omar Rasheed Zeyadah, Amjad Jaber Alqahtani, Sara Al Fliti, Nahid Akhtar, Suraj Sharma, Andrea Petta, Luigi Cavallo, Romina Oliva, Mohit Chawla
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Journal Nucleic Acids Research
Year 2026
DOI
10.1093/nar/gkag1080
URL
https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkag1080/72614248/gkag1080.pdf
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