ArticlePLoS computational biology2023
Deciphering the RRM-RNA recognition code: A computational analysis.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 20 citations in OpenAlex.
- Leishmania major virulence attenuation in vitro: An old conundrum revisited in the omics era.PLoS neglected tropical diseases · 2026Article
- L1TD1 promotes colorectal mucinous adenocarcinoma progression by enhancing ABCC3 mRNA stability.Oncogene · 2026Article
- The RRM domains of PARP14 mediate replication fork degradation in BRCA2-deficient cells.NAR cancer · 2026Article
- La protein binding to telomerase RNA supports an evolutionary relationship between plant and ciliate telomerase pathways.Nucleic acids research · 2026Article
- caRBP-Pred: Leveraging Protein Language Models for the Prediction of Chromatin-Associated RNA-Binding Proteins.Computational and structural biotechnology journal · 2026Article
- Deciphering the RNA recognition by Musashi-1 to design protein and RNA variants for in vitro and in vivo applications.Nucleic acids research · 2025Article
- RRMScorer: A web server for predicting RNA recognition motif binding preferences.Nucleic acids research · 2025Article
- The RRM domain-containing protein Rbp3 interacts with ribosomes and the 3' ends of mRNAs encoding photosynthesis proteins.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Regulatory Effects of RNA-Protein Interactions Revealed by Reporter Assays of Bacteria Grown on Solid Media.Biosensors · 2025Article
- Deep mutational scanning of the Trypanosoma brucei developmental regulator RBP6 reveals an essential disordered region influenced by positive residues.Nature communications · 2025Article
- Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts.PLoS computational biology · 2024Article
- Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper.Bioinformatics (Oxford, England) · 2024Article
- Analysis of the inter-domain orientation of tandem RRM domains with diverse linkers: connecting experimental with AlphaFold2 predicted models.NAR genomics and bioinformatics · 2024Article
- Origin of ribonucleotide recognition motifs through ligand mimicry at early earth.RNA biology · 2024Review
- Research Progress on the Structural and Functional Roles of hnRNPs in Muscle Development.Biomolecules · 2023Review
- Article
- CroMaSt: a workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment.Bioinformatics advances · 2023Article
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA recognition motifs (RRM) are the most prevalent class of RNA binding domains in eucaryotes. Their RNA binding preferences have been investigated for almost two decades, and even though some RRM domains are now very well described, their RNA recognition code has remained elusive. An increasing number of experimental structures of RRM-RNA complexes has become available in recent years. Here, we perform an in-depth computational analysis to derive an RNA recognition code for canonical RRMs. We present and validate a computational scoring method to estimate the binding between an RRM and a single stranded RNA, based on structural data from a carefully curated multiple sequence alignment, which can predict RRM binding RNA sequence motifs based on the RRM protein sequence. Given the importance and prevalence of RRMs in humans and other species, this tool could help design RNA binding motifs with uses in medical or synthetic biology applications, leading towards the de novo design of RRMs with specific RNA recognition.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.