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Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models


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

Scientific discipline (Law 2.0)

[2.3] Information and communication technology
[7.6] Chemical sciences

Year of publication


Published in

International Journal of Molecular Sciences

Journal year: 2022 | Journal volume: vol. 23 | Journal number: iss. 17

Article type

scientific article

Publication language


  • multi-model evaluation
  • RNA 3D structures
  • 3D structure prediction
  • reference-free analysis
  • SARS-CoV-2 genome
  • 5′-UTR
  • 3′-UTR

EN RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5′- and 3′-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.

Date of online publication


Pages (from - to)

9630-1 - 9630-20





Article Number: 9630

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

Ministry points / journal


Impact Factor


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