ArticlePLoS computational biology2016
Template-Based Modeling of Protein-RNA Interactions.
Article in PLoS computational biology, 2016. 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, 47 citations in OpenAlex.
- PRIME-BSPre: a genome-wide protein-RNA binding sites prediction method based on templates.BMC genomics · 2026Article
- Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models.Cell systems · 2025Article
- Aptamers as Potential Inhibitors of Ethylene Biosynthesis: Identification and In Silico Selection.International journal of molecular sciences · 2025Article
- Dockground: The Resource Expands to Protein-RNA Interactome.Journal of molecular biology · 2025Article
- Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts.PLoS computational biology · 2024Article
- RBProkCNN: Deep learning on appropriate contextual evolutionary information for RNA binding protein discovery in prokaryotes.Computational and structural biotechnology journal · 2024Article
- Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi.Nature communications · 2024Article
- Transcriptome-wide identification of single-stranded RNA binding proteins.Chemical science · 2023Article
- US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes.Nature methods · 2022Article
- 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
- DNA- and RNA-Binding Proteins Linked Transcriptional Control and Alternative Splicing Together in a Two-Layer Regulatory Network System of Chronic Myeloid Leukemia.Frontiers in molecular biosciences · 2022Article
- RR3DD: an RNA global structure-based RNA three-dimensional structural classification database.RNA biology · 2021Article
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- A novel antiviral lncRNA, EDAL, shields a T309 O-GlcNAcylation site to promote EZH2 lysosomal degradation.Genome biology · 2020Article
- PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction.Communications biology · 2020Article
- Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- RMalign: an RNA structural alignment tool based on a novel scoring function RMscore.BMC genomics · 2019Article
- Computational approaches to macromolecular interactions in the cell.Current opinion in structural biology · 2019Review
- Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.
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Registered trials
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.