ArticleNucleic acids research2021
catRAPID omics v2.0: going deeper and wider in the prediction of protein-RNA interactions.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers.
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133 citing papers in PubMed, 262 citations in OpenAlex.
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- Systems-level analysis predicts no autotrophy-linked protein-RNA interactions in Clostridium autoethanogenum.Nature communications · 2026Article
- Hypoxia-induced exosomal LNCOC1 orchestrates bladder cancer progression via the YBX1/PIK3CA axis and serves as a potential liquid biopsy biomarker.Cellular oncology (Dordrecht, Netherlands) · 2026Article
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- SAM68 is a multifunctional post-transcriptional regulator of cardiomyocyte differentiation.Nucleic acids research · 2026Article
- scRAPID-web: a web server for predicting protein-RNA interactions from single-cell transcriptomics.BMC genomics · 2026Article
- PTBP1 controls miRNA loading on target RNAs: lessons from the CyCoNP lncRNA.RNA (New York, N.Y.) · 2026Article
- A novel deep learning-driven framework for improving lncRNA comprehensive annotation with LncADeep 2.0.Bioinformatics (Oxford, England) · 2026Article
- LncRNA-Gm5532 deficiency alleviates bone resorption by inhibiting mitochondrial respiration through iASPP/NRF2.Cell biology and toxicology · 2026Article
- Interplay between RNA-protein interactions and RNA structures in gene regulation.FEBS open bio · 2026Review
- PTBP1-mediated inhibition of circular RNA SCMH1 biogenesis impairs brain recovery after ischemic stroke.Theranostics · 2026Article
- Mechanism of ribonucleic acid-binding protein ILF2 in promoting diabetic foot ulcer wound healing via regulating the nucleophosmin 1/NF-κB axis.Burns & trauma · 2026Article
73 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prediction of protein-RNA interactions is important to understand post-transcriptional events taking place in the cell. Here we introduce catRAPID omics v2.0, an update of our web server dedicated to the computation of protein-RNA interaction propensities at the transcriptome- and RNA-binding proteome-level in 8 model organisms. The server accepts multiple input protein or RNA sequences and computes their catRAPID interaction scores on updated precompiled libraries. Additionally, it is now possible to predict the interactions between a custom protein set and a custom RNA set. Considerable effort has been put into the generation of a new database of RNA-binding motifs that are searched within the predicted RNA targets of proteins. In this update, the sequence fragmentation scheme of the catRAPID fragment module has been included, which allows the server to handle long linear RNAs and to analyse circular RNAs. For the top-scoring protein-RNA pairs, the web server shows the predicted binding sites in both protein and RNA sequences and reports whether the predicted interactions are conserved in orthologous protein-RNA pairs. The catRAPID omics v2.0 web server is a powerful tool for the characterization and classification of RNA-protein interactions and is freely available at http://service.tartaglialab.com/page/catrapid_omics2_group along with documentation and tutorial.
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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.