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RNAspider: a webserver to analyze entanglements in RNA 3D structures.
Kamil Luwanski1, Vladyslav Hlushchenko1, Mariusz Popenda2
1Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
Nucleic Acids Research
|March 29, 2022
Summary
RNAspider is a new web server that identifies, classifies, and visualizes complex RNA 3D structure entanglements. This tool aids in studying unique RNA topologies and knot-like folds in viral genomes.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Advancements in experimental and computational methods allow for the study of large, complex RNA 3D structures.
- Complex RNA structures exhibit unique properties, including entanglements and knot-like folds, particularly in RNA viruses.
- A prior classification of RNA entanglements based on topology and entangled elements was established.
Purpose of the Study:
- To introduce RNAspider, a novel web server for the automated analysis of RNA 3D structures.
- To enable the identification, classification, and visualization of primary and higher-order entanglements in RNA.
- To support the analysis of unusual topologies, including those in pseudoknotted RNA structures.
Main Methods:
- Development of a web server, RNAspider, for automated analysis of RNA 3D models.
- Application of algorithms to identify and classify topological features of RNA entanglements.
- Visualization tools integrated into the web server for user-friendly interpretation of results.
Main Results:
- RNAspider successfully identifies and classifies various types of entanglements in RNA tertiary structures.
- The tool processes RNA 3D models derived from experimental data or computational predictions.
- Support for analyzing complex and uncommon topologies, such as those found in pseudoknots, is provided.
Conclusions:
- RNAspider offers a user-friendly, publicly accessible platform for exploring complex RNA structural features.
- The tool advances the study of RNA topology, entanglements, and knot-like folds.
- Facilitates deeper understanding of RNA structural diversity and function, especially in viral systems.
