ArticleNucleic acids research2021
Entanglements of structure elements revealed in RNA 3D models.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- The MODNAP benchmark set for modeling ribose-based modified nucleic acid and nucleic acid-protein complexes: a case study with AlphaFold 3.Nucleic acids research · 2026Article
- Disruption of the Nucleolin-CXCR4 interaction by the DNA aptamer HY-4 halts colorectal cancer metastasis.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Unknotting RNA: A method to resolve computational artifacts.PLoS computational biology · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Assessing interface accuracy in macromolecular complexes.PloS one · 2025Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- RNAtango: Analysing and comparing RNA 3D structures via torsional angles.PLoS computational biology · 2024Article
- Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.Nucleic acids research · 2024Article
- Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.Nucleic acids research · 2024Article
- RNAhugs web server for customized 3D RNA structure alignment.Nucleic acids research · 2024Article
- Knotted artifacts in predicted 3D RNA structures.PLoS computational biology · 2024Article
- Knotify_V2.0: Deciphering RNA Secondary Structures with H-Type Pseudoknots and Hairpin Loops.Genes · 2024Article
- Machine learning for RNA 2D structure prediction benchmarked on experimental data.Briefings in bioinformatics · 2023Review
- RNAloops: a database of RNA multiloops.Bioinformatics (Oxford, England) · 2022Article
- Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.International journal of molecular sciences · 2022Article
- RNAspider: a webserver to analyze entanglements in RNA 3D structures.Nucleic acids research · 2022Article
- Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions.RNA (New York, N.Y.) · 2022Article
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Computational methods to predict RNA 3D structure have more and more practical applications in molecular biology and medicine. Therefore, it is crucial to intensify efforts to improve the accuracy and quality of predicted three-dimensional structures. A significant role in this is played by the RNA-Puzzles initiative that collects, evaluates, and shares RNAs built computationally within currently nearly 30 challenges. RNA-Puzzles datasets, subjected to multi-criteria analysis, allow revealing the strengths and weaknesses of computer prediction methods. Here, we study the issue of entangled RNA fragments in the predicted RNA 3D structure models. By entanglement, we mean an arrangement of two structural elements such that one of them passes through the other. We propose the classification of entanglements driven by their topology and components. It distinguishes two general classes, interlaces and lassos, and subclasses characterized by element types-loops, dinucleotide steps, open single-stranded fragments-and puncture multiplicity. Our computational pipeline for entanglement detection, applied for 1,017 non-redundant models from RNA-Puzzles, has shown the frequency of different entanglements and allowed identifying 138 structures with intersected assemblies.
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