ArticleBMC biology2025
RBPsuite 2.0: an updated RNA-protein binding site prediction suite with high coverage on species and proteins based on deep learning.
Article in BMC biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Extracellular Vesicles: Classification, Biological Functions, Diseases, and Therapeutic Opportunities.MedComm · 2026Review
- Review
- Functional Variants of the RAD51 Gene Contribute to Susceptibility to Non-Syndromic Orofacial Clefts in a Han Chinese Population.Orthodontics & craniofacial research · 2026Article
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Disrupting SRSF10-dependent BCAT2 exon skipping reprograms tumor-associated macrophages and enhances anti-PD-1 efficacy in gastric cancer.Cell death & disease · 2026Article
- Glycolytic Reprogramming Mediated by the OTUD4-FXR1-HIF1A Axis Drives Gastric Cancer Progression.International journal of biological sciences · 2026Article
- RNA-binding protein HnRNPU regulates proliferation and ferroptosis in colon adenocarcinoma by stabilizing the mRNA of system xcExperimental & molecular medicine · 2025Article
- Base-resolution binding profile prediction of proteins on RNAs with deep learning.Nucleic acids research · 2025Article
- RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA-protein binding sites prediction.BMC bioinformatics · 2025Article
- LncRNA HOTAIR Interaction With WTAP Promotes m6A Methyltransferase Complex Assembly and Posterior Capsule Opacification Formation by Increasing THBS1.Investigative ophthalmology & visual science · 2025Article
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Abstract
backgroundRNA-binding proteins (RBPs) play crucial roles in many biological processes, and computationally identifying RNA-RBP interactions provides insights into the biological mechanism of diseases associated with RBPs.
resultsTo make the RBP-specific deep learning-based RBP binding sites prediction methods easily accessible, we developed an updated easy-to-use webserver, RBPsuite 2.0, with an updated web interface for predicting RBP binding sites from linear and circular RNA sequences. RBPsuite 2.0 has a higher coverage on the number of supported RBPs and species compared to the original RBPsuite, supporting an increased number of RBPs from 154 to 353 and expanding the supported species from one to seven. Additionally, RBPsuite 2.0 replaces the CRIP built into RBPsuite 1.0 with iDeepC, a more accurate RBP binding site predictor for circular RNAs. Furthermore, RBPsuite 2.0 estimates the contribution score of individual nucleotides on the input sequences as potential binding motifs and links to the UCSC browser track for better visualization of the prediction results.
conclusionsRBPsuite 2.0 is an updated, more comprehensive webserver for predicting RBP binding sites in both linear and circular RNA sequences. It supports more RBPs and species and provides more accurate predictions for circular RNAs. The tool is freely available at http://www.csbio.sjtu.edu.cn/bioinf/RBPsuite/ .
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