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Affinity and kinetic constants

The equilibrium dissociation constant (K_D) quantifies binding affinity; a lower K_D indicates tighter binding. For a reversible 1:1 interaction, K_D = k_off/k_on, where k_on is the association rate constant (M⁻¹s⁻¹) and describes how quickly the binding partners associate, whereas k_off is the dissociation rate constant (s⁻¹) and describes how quickly the complex dissociates.

Inclusion Criteria

RNAffinityDB curates direct experimental measurements of binding between one defined protein construct and one single-stranded RNA with a defined sequence of canonical ribonucleotides. Records are included when the binding outcome is reported as an affinity value, a one-sided measurement limit, or an explicit non-binding observation.

Protein constructs represented in the database include full-length proteins, isolated domains, truncations, and engineered variants when the protein identity, construct boundaries, and reported sequence variants can be resolved. RNA sequences are at least four nucleotides long and are composed of canonical ribonucleotides (A, C, G, and U). Fluorescent or biotin labels used solely for experimental detection are permitted.

The collection excludes multi-protein complexes, ribosome assemblies, RNA duplexes, RNAs containing chemically modified ribonucleotides, mixed RNA-DNA constructs, and records with ambiguous molecular assignments.

Data Sources and Tool Citations

Protein domain and functional annotation information is derived from the UniProt database.

UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Research 53:D609-D617 (2025).

Predicted structures are generated with AlphaFold 3 and packaged as mmCIF files.

Abramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., Ronneberger, O., Willmore, L., Ballard, A.J., Bambrick, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630:493-500 (2024).