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

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dc.abstract.enRNA 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.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorChandran, Nithin
dc.contributor.authorMukherjee, Sunandan
dc.contributor.authorBujnicki, Janusz
dc.contributor.authorWirecki, Tomasz
dc.contributor.authorPopenda, Mariusz
dc.contributor.authorSarzyńska, Joanna
dc.contributor.authorPachulska-Wieczorek, Katarzyna
dc.contributor.authorGumna, Julita
dc.contributor.authorŻok, Tomasz
dc.contributor.authorRybarczyk, Agnieszka
dc.contributor.authorAdamiak, Ryszard
dc.contributor.authorChen, Shi-Jie
dc.contributor.authorNithin, Chandran
dc.contributor.authorMiao, Zhichao
dc.contributor.authorZhang, Sicheng
dc.contributor.authorGhosh, Pritha
dc.contributor.authorDing, Feng
dc.contributor.authorPonce-Salvatierra, Almudena
dc.contributor.authorWesthof, Eric
dc.contributor.authorLi, Jun
dc.contributor.authorZhang, Dong
dc.contributor.authorSzachniuk, Marta
dc.contributor.authorAntczak, Maciej
dc.date.accessioned2024-01-24T19:52:43Z
dc.date.available2024-01-24T19:52:43Z
dc.date.issued2022
dc.description.accesstimeBEFORE_PUBLICATION
dc.description.financeNie dotyczy
dc.description.number17
dc.description.versionFINAL_PUBLISHED
dc.description.volume23
dc.identifier.doi10.3390/IJMS23179630
dc.identifier.issn1422-0067
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/103478
dc.identifier.weblinkhttps://www.mdpi.com/1422-0067/23/17/9630
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofInternational Journal of Molecular Sciences
dc.relation.pages9630
dc.rightsCC-BY-ND
dc.sciencecloudnosend
dc.subject.en5′-UTR
dc.subject.enreference-free analysis
dc.subject.enRNA 3D structures
dc.subject.en3′-UTR
dc.subject.enmulti-model evaluation
dc.subject.enSARS-CoV-2 genome
dc.subject.en3D structure prediction
dc.titleComputational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models
dc.typeJournalArticle
dspace.entity.typePublication