ArticleNucleic acids research2022
RNAspider: a webserver to analyze entanglements in RNA 3D structures.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 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
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- Mol* web molecular graphics engine.Protein science : a publication of the Protein Society · 2026Article
- A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions.Nucleic acids research · 2026Article
- DRfold2 is a deep learning-based tool that enables efficient and accurate RNA structure prediction.PLoS biology · 2026Article
- RNAtive to recognize native-like structure in a set of RNA 3D models.Bioinformatics (Oxford, England) · 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
- Knotted artifacts in predicted 3D RNA structures.PLoS computational biology · 2024Article
- Examples of Structural Motifs in Viral Genomes and Approaches for RNA Structure Characterization.International journal of molecular sciences · 2022Review
- Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.International journal of molecular sciences · 2022Article
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8 authors.
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Abstract
Advances in experimental and computational techniques enable the exploration of large and complex RNA 3D structures. These, in turn, reveal previously unstudied properties and motifs not characteristic for small molecules with simple architectures. Examples include entanglements of structural elements in RNA molecules and knot-like folds discovered, among others, in the genomes of RNA viruses. Recently, we presented the first classification of entanglements, determined by their topology and the type of entangled structural elements. Here, we introduce RNAspider - a web server to automatically identify, classify, and visualize primary and higher-order entanglements in RNA tertiary structures. The program applies to evaluate RNA 3D models obtained experimentally or by computational prediction. It supports the analysis of uncommon topologies in the pseudoknotted RNA structures. RNAspider is implemented as a publicly available tool with a user-friendly interface and can be freely accessed at https://rnaspider.cs.put.poznan.pl/.
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