ArticleGenome biology2014
GraphProt: modeling binding preferences of RNA-binding proteins.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 150 papers.
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Who cites it
150 citing papers in PubMed.
- K-attention: a biologically informed attention operator for data-efficient sequence-based omics modeling.Briefings in bioinformatics · 2026Article
- A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function.Nature biotechnology · 2026Article
- A protocol for single-sequence protein-RNA complex structure prediction using ProRNA3D-single.STAR protocols · 2026Article
- Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling.Nature communications · 2026Article
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- Augmented prediction of multi-species protein-RNA interactions using evolutionary conservation of RNA-binding proteins.Nature communications · 2026Article
- Generalizable deep-learning-based mRNA-protein interaction prediction strongly depends on protein diversity.Journal of cheminformatics · 2026Article
- PRIME-BSPre: a genome-wide protein-RNA binding sites prediction method based on templates.BMC genomics · 2026Article
- Struct2GO-Enhanced: Multimodal Graph Attention Improves Protein Function Prediction.Journal of chemical information and modeling · 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 Structure and Its Function.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- RNA-binding proteins connect Exon usage to the chromatin.NAR genomics and bioinformatics · 2025Article
- Kideraspa: designing variants of staphylococcal protein a based on a diffusion model with kidera factors.Journal of computer-aided molecular design · 2025Article
- Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models.Cell systems · 2025Article
- PaRPI predicts RNA-Protein interactions from cross-protocol and cross-batch RNA-binding protein datasets.Communications biology · 2025Article
- Review
- RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA-protein binding sites prediction.BMC bioinformatics · 2025Article
- Nuclear Retention of mRNAs Through Paraspeckle Protein Binding to a Sequence Determinant in 3'UTR.International journal of molecular sciences · 2025Article
- LncPTPred: predicting lncRNA-protein interaction based on crosslinking and immunoprecipitation (CLIP-Seq) data.Briefings in bioinformatics · 2025Article
90 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. We benchmark GraphProt, demonstrating that the modeled binding preferences conform to the literature, and showcase the biological relevance and two applications of GraphProt models. First, estimated binding affinities correlate with experimental measurements. Second, predicted Ago2 targets display higher levels of expression upon Ago2 knockdown, whereas control targets do not. Computational binding models, such as those provided by GraphProt, are essential for predicting RBP binding sites and affinities in all tissues. GraphProt is freely available at http://www.bioinf.uni-freiburg.de/Software/GraphProt.
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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.