ArticleCommunications biology2020
PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction.
Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- PRIME-BSPre: a genome-wide protein-RNA binding sites prediction method based on templates.BMC genomics · 2026Article
- RNA-protein interaction prediction without high-throughput data: An overview and benchmark ofComputational and structural biotechnology journal · 2024Article
- Transcriptome-wide identification of single-stranded RNA binding proteins.Chemical science · 2023Article
- Review
- Protein-RNA interaction prediction with deep learning: structure matters.Briefings in bioinformatics · 2022Article
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
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Authors and funding
5 authors.
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Abstract
Protein-RNA interaction participates in many biological processes. So, studying protein-RNA interaction can help us to understand the function of protein and RNA. Although the protein-RNA 3D3D model, like PRIME, was useful in building 3D structural complexes, it can't be used genome-wide, due to lacking RNA 3D structures. To take full advantage of RNA secondary structures revealed from high-throughput sequencing, we present PRIME-3D2D to predict binding sites of protein-RNA interaction. PRIME-3D2D is almost as good as PRIME at modeling protein-RNA complexes. PRIME-3D2D can be used to predict binding sites on PDB data (MCC = 0.75/0.70 for binding sites in protein/RNA) and transcription-wide (MCC = 0.285 for binding sites in RNA). Testing on PDB and yeast transcription-wide data show that PRIME-3D2D performs better than other binding sites predictor. So, PRIME-3D2D can be used to predict the binding sites both on PDB and genome-wide, and it's freely available.
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Registered trials
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