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Peer-reviewedCC BY 4.0Nucleic Acids Research

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

  • Wenjun Lin1
  • Zhaoming Chen2
  • Yao Li2
  • Hui Wang2
  • He Huang2
  • Hongwang Xiao2,3
  • Andres Jäschke1
  • Qiwei Ye2
  • Yaqing Zhang1,2
  1. 1Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University , Heidelberg 69120 ,
  2. 2Beijing Academy of Artificial Intelligence (BAAI) , Beijing 100090 ,
  3. 3State Key Laboratory of Multimedia Information Processing, Peking University , Beijing 100871 ,
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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.

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Cite

BibTeXRIS
BibTeX
@article{lin2026rnaffinitydb,
  title = {{RNAffinityDB: a curated database of experimental RNA–protein binding affinities}},
  author = {Wenjun Lin and Zhaoming Chen and Yao Li and Hui Wang and He Huang and Hongwang Xiao and Andres Jäschke and Qiwei Ye and Yaqing Zhang},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag984},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag984/8937184},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - RNAffinityDB: a curated database of experimental RNA–protein binding affinities
AU  - Wenjun Lin
AU  - Zhaoming Chen
AU  - Yao Li
AU  - Hui Wang
AU  - He Huang
AU  - Hongwang Xiao
AU  - Andres Jäschke
AU  - Qiwei Ye
AU  - Yaqing Zhang
PY  - 2026
DA  - 2026/10/19
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag984
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag984/8937184
AB  - 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.
SN  - 0305-1048
SN  - 1362-4962
ER  -