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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...

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Autores principales: Luwanski, Kamil, Hlushchenko, Vladyslav, Popenda, Mariusz, Zok, Tomasz, Sarzynska, Joanna, Martsich, Daniil, Szachniuk, Marta, Antczak, Maciej
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
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/.
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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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