ArticleInternational journal of molecular sciences2022
Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.
Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 27 citations in OpenAlex.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Review
- In Silico Ligand-Based Screening of PDB Database for Searching Unique Motifs Against SARS-CoV-2.Biomolecules · 2026Article
- Conformational Analysis and Structure-Altering Mutations of the HIV-1 Frameshifting Element.International journal of molecular sciences · 2025Article
- Unknotting RNA: A method to resolve computational artifacts.PLoS computational biology · 2025Article
- When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines.Computational and structural biotechnology journal · 2025Article
- Toward Increasing the Credibility of RNA Design.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- RNAtango: Analysing and comparing RNA 3D structures via torsional angles.PLoS computational biology · 2024Article
- Article
- Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.Nucleic acids research · 2024Article
- Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes.Nucleic acids research · 2024Article
- Unveiling hidden structural patterns in the SARS-CoV-2 genome: Computational insights and comparative analysis.PloS one · 2024Article
- LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules.Nucleic acids research · 2023Article
- When will RNA get its AlphaFold moment?Nucleic acids research · 2023Article
- CovidShiny: An Integrated Web Tool for SARS-CoV-2 Mutation Profiling and Molecular Diagnosis Assay Evaluation In Silico.Viruses · 2023Article
- The Highly Conserved Stem-Loop II Motif Is Dispensable for SARS-CoV-2.Journal of virology · 2023Article
- Mutagenesis and structural studies reveal the basis for the specific binding of SARS-CoV-2 SL3 RNA element with human TIA1 protein.Nature communications · 2023Article
- The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements.Nature communications · 2023Article
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Authors and funding
22 authors at 7 institutions in 4 countries.
Funding
Abstract
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.
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