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RNAspider: a webserver to analyze entanglements in RNA 3D structures
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 elemen...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252836/ https://www.ncbi.nlm.nih.gov/pubmed/35349710 http://dx.doi.org/10.1093/nar/gkac218 |
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author | Luwanski, Kamil Hlushchenko, Vladyslav Popenda, Mariusz Zok, Tomasz Sarzynska, Joanna Martsich, Daniil Szachniuk, Marta Antczak, Maciej |
author_facet | Luwanski, Kamil Hlushchenko, Vladyslav Popenda, Mariusz Zok, Tomasz Sarzynska, Joanna Martsich, Daniil Szachniuk, Marta Antczak, Maciej |
author_sort | Luwanski, Kamil |
collection | PubMed |
description | 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/. |
format | Online Article Text |
id | pubmed-9252836 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-92528362022-07-05 RNAspider: a webserver to analyze entanglements in RNA 3D structures Luwanski, Kamil Hlushchenko, Vladyslav Popenda, Mariusz Zok, Tomasz Sarzynska, Joanna Martsich, Daniil Szachniuk, Marta Antczak, Maciej Nucleic Acids Res Web Server Issue 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/. Oxford University Press 2022-03-29 /pmc/articles/PMC9252836/ /pubmed/35349710 http://dx.doi.org/10.1093/nar/gkac218 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Web Server Issue Luwanski, Kamil Hlushchenko, Vladyslav Popenda, Mariusz Zok, Tomasz Sarzynska, Joanna Martsich, Daniil Szachniuk, Marta Antczak, Maciej RNAspider: a webserver to analyze entanglements in RNA 3D structures |
title | RNAspider: a webserver to analyze entanglements in RNA 3D structures |
title_full | RNAspider: a webserver to analyze entanglements in RNA 3D structures |
title_fullStr | RNAspider: a webserver to analyze entanglements in RNA 3D structures |
title_full_unstemmed | RNAspider: a webserver to analyze entanglements in RNA 3D structures |
title_short | RNAspider: a webserver to analyze entanglements in RNA 3D structures |
title_sort | rnaspider: a webserver to analyze entanglements in rna 3d structures |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252836/ https://www.ncbi.nlm.nih.gov/pubmed/35349710 http://dx.doi.org/10.1093/nar/gkac218 |
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