ArticleNucleic acids research2023
PrismNet: predicting protein-RNA interaction using in vivo RNA structural information.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling.Nature communications · 2026Article
- Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning.Briefings in bioinformatics · 2026Article
- PRIME-BSPre: a genome-wide protein-RNA binding sites prediction method based on templates.BMC genomics · 2026Article
- Sequence-Based Models for RNA-Protein Interactions Imputation Might Be Insufficient for Novel Signal Prediction in eCLIP Data.International journal of molecular sciences · 2026Article
- RNA-binding proteins connect Exon usage to the chromatin.NAR genomics and bioinformatics · 2025Article
- ERNIE-RNA: an RNA language model with structure-enhanced representations.Nature communications · 2025Article
- Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3'UTR isoform diversity.Genome biology · 2025Article
- Biomolecular Interaction Prediction: The Era of AI.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Base-resolution binding profile prediction of proteins on RNAs with deep learning.Nucleic acids research · 2025Article
- RRMScorer: A web server for predicting RNA recognition motif binding preferences.Nucleic acids research · 2025Article
- Stem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshifting.Signal transduction and targeted therapy · 2025Article
- RBPsuite 2.0: an updated RNA-protein binding site prediction suite with high coverage on species and proteins based on deep learning.BMC biology · 2025Article
- Article
- Identification of antiviral RNAi regulators, ILF3/DHX9, recruit at ZIKV stem loop B to protect against ZIKV induced microcephaly.Nature communications · 2025Article
- Emerging RNA-centric technologies to probe RNA-protein interactions: importance in decoding the life cycle of positive sense single strand RNA viruses and antiviral discovery.Frontiers in cellular and infection microbiology · 2025Review
- EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events.Bioinformatics (Oxford, England) · 2024Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- Review
- RNA structure: implications in viral infections and neurodegenerative diseases.Advanced biotechnology · 2024Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fundamental to post-transcriptional regulation, the in vivo binding of RNA binding proteins (RBPs) on their RNA targets heavily depends on RNA structures. To date, most methods for RBP-RNA interaction prediction are based on RNA structures predicted from sequences, which do not consider the various intracellular environments and thus cannot predict cell type-specific RBP-RNA interactions. Here, we present a web server PrismNet that uses a deep learning tool to integrate in vivo RNA secondary structures measured by icSHAPE experiments with RBP binding site information from UV cross-linking and immunoprecipitation in the same cell lines to predict cell type-specific RBP-RNA interactions. Taking an RBP and an RNA region with sequential and structural information as input ('Sequence & Structure' mode), PrismNet outputs the binding probability of the RBP and this RNA region, together with a saliency map and a sequence-structure integrative motif. The web server is freely available at http://prismnetweb.zhanglab.net.
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