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Structured query across RNA–ligand complexes. Combine filters by structure, affinity, ligand chemistry, and RNA sequence.

RNA target name Search by RNA target, subclass, or display name. RNA class Select the functional RNA class, such as riboswitch or aptamer. Kd measurement method Experimental method used to determine K_d, such as ITC or fluorescence.

19F NMR titrations 1H NMR titrations 2AP fluorescence assay ^19F NMR chemical-shift perturbation titration of SMN-C5 with the RNA duplex. Circular dichroism (CD) spectroscopy Competition binding kinetics Competition-binding assay Competition-binding assay based on fluorescence anisotropy Competition-binding assay using BODIPY-labeled erythromycin DMS chemical probing (footprinting) assay DMS footprinting + Phosphorimager quantification Electrophoretic mobility shift assay (EMSA) with radiolabeled ligand Elution of 32P-labeled RNA from a column Equilibrium binding assay using radiolabeled [14C]-ERY Equilibrium dialysis Equilibrium dialysis using radiolabeled [β-33P]-PRPP. Equilibrium filtration ESI-FT-ICR Mass Spectrometry Binding Assay Fluorescence Fluorescence (using 2-aminopurine labeled A-site RNA) Fluorescence anisotropy Fluorescence anisotropy titration Fluorescence assay Fluorescence based binding/Fluorescence Titration Fluorescence binding titrations Fluorescence quenching Fluorescence quenching assay Fluorescence spectroscopy Fluorescence titration Fluorescence titrations Fluorescence-based RNAligand binding assay Fluorescene spectroscopy Fluoroscence Gel-Shift Analysis In-line probing In-line probing analyzed with curve fitting (Origin software). In-line probing assay In-vitro binding assays Intrinsic ligand fluorescence Isocratic elution and by equilibrium gel filtration ITC Ligand-detected NMR titration (1H NMR) with Bloch-McConnell lineshape simulation Microscale thermophoresis (MST) Nitrocellulose filter technique NMR binding assay. NMR Chemical Shift Perturbation (CSP) Titration NMR chemical shift titration using a quadratic tight-binding model (1:1 binding, fast exchange). NMR titration for Kd determination using a one-site binding model NMR titration of RNA with MTX Quantitative dimethyl sulfate footprinting Quantitative Footprinting Radiolabeled ligand equilibrium binding assay Sedimentation method. Serial dilutions of Corn RNA using native PAGE SHAPE Size-exclusion filtration assay Solid-phase equilibrium binding assay Spin-filtration method SPR Steady-state fluorescence Ultrafiltration method UVâvis absorbance spectroscopy X-ray crystallographic occupancy (indirect)

pK_d minimum Lowest pK_d to include; cannot exceed the maximum. pK_d maximum Highest pK_d to include; cannot be below the minimum.

PDB ID/Extended PDB ID 4-character PDB accession or Extended PDB entry identifier. CCD ligand ID Chemical Component Dictionary (CCD) code, such as JS4 or GLY. Ligand compound name Full chemical or molecule name. Resolution minimum (Å) Lowest resolution to include; cannot exceed the maximum. Resolution maximum (Å) Highest resolution to include; cannot be below the minimum. Structure determination method Experimental method used to solve the structure, such as X-ray, cryo-EM, or NMR.

ELECTRON MICROSCOPY SOLID-STATE NMR SOLUTION NMR X-RAY DIFFRACTION

CCD ligand ID Chemical Component Dictionary (CCD) code. Ligand compound name Full ligand or small-molecule name. PubChem CID PubChem compound identifier.

SMILES Search by SMILES string or fragment. InChIKey Search by full InChIKey or prefix. Minimum molecular weight (Da) Lowest molecular weight to include; cannot exceed the maximum. Maximum molecular weight (Da) Highest molecular weight to include; cannot be below the minimum.

RNA sequence Search by RNA subsequence using A, C, G, and U; T is treated as U.

RNA class Select the functional RNA class. RNA target name Search by RNA target, subclass, or display name. RNA length minimum (nt) Shortest RNA length to include; cannot exceed the maximum. RNA length maximum (nt) Longest RNA length to include; cannot be below the minimum.

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ARIEL — Affinity Resource for Interactions of RNA & Ligands — Dataset v2026-10-11 19:27 UTC

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