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Article


Title

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Authors

[ 1 ] Wydział Informatyki i Telekomunikacji, Politechnika Poznańska | [ 2 ] Instytut Informatyki, Wydział Informatyki i Telekomunikacji, Politechnika Poznańska | [ S ] student | [ P ] employee

Scientific discipline (Law 2.0)

[2.3] Information and communication technology

Year of publication

2022

Published in

Nucleic Acids Research

Journal year: 2022 | Journal volume: vol. 50 | Journal number: iss. W1

Article type

scientific article

Publication language

english

Keywords
EN
  • RNA 3D structure
  • entanglement identification
  • lasso
  • interlace
  • knot-like fold
Abstract

EN 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/.

Date of online publication

29.03.2022

Pages (from - to)

W663 - W669

DOI

10.1093/nar/gkac218

URL

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac218/6555428

License type

CC BY (attribution alone)

Open Access Mode

open journal

Open Access Text Version

final published version

Date of Open Access to the publication

in press

Points of MNiSW / journal

200.0

Impact Factor

16.971 [List 2020]

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