Work

RNAffinityDB: a curated database of experimental RNA–protein binding affinities

Year: 2026

Type: article

Abstract: RNA-protein interactions modulate RNA function and direct RNA fate in cells. Over the past several decades, experimental studies have yielded a substantial but fragmented record of binding affinity measurements for defined RNA-protein pairs, obscuring a unified view of how sequence determinants shape binding strength. Here, we present RNAffinityDB, a curated database of experimental RNA-protein binding affinities. Its curation framework anchors each measurement to one defined protein construct and one single-stranded RNA with a defined sequence of canonical ribonucleotides. The current release comprises 10 ,016 construct-resolved records from 1,055 source publications, covering 3,057 protein constructs and 4,638 RNA sequences. The database preserves affinity values and measurement boundaries as reported, together with non-binding observations. The web interface enables direct retrieval by protein identity or RNA sequence and semantic queries on biological function, with records linked to UniProt annotations and interactive visualizations of AlphaFold 3-predicted complex structures. RNAffinityDB supports systematic analysis of sequence-affinity relationships and the downstream development of RNA-protein affinity models. RNAffinityDB is freely available at https://www.ultrarnalab.com/RNAffinityDB.php.

Source: Nucleic Acids Research

DOI: 10.1093/nar/gkag984