ArticleNucleic acids research2021
De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 82 citations in OpenAlex.
- Integrative in silico and in vitro screening of small molecules targeting RNA.Current protocols · 2026Article
- A potential RNA-RNA distal interaction competing with a functional pseudoknot in the 3'-untranslated region of SARS-like coronaviruses.Nucleic acids research · 2026Article
- Integrative In Silico and In Vitro Screening of Low Molecular Weight Compounds Targeting SARS-CoV-2 RNA Elements.Chembiochem : a European journal of chemical biology · 2025Article
- Structural heterogeneity and dynamics in the apical stem loop of s2m from SARS-CoV-2 Delta by an integrative NMR spectroscopy and MD simulation approach.Nucleic acids research · 2025Article
- Unraveling the Amplification-Free Quantitative Detection of Viral RNA in Nasopharyngeal Swab Samples Using a Compact Electrochemical Rapid Test Device.Analytical chemistry · 2025Article
- SARS-CoV-2 point mutations are over-represented in terminal loops of RNA stem-loop structures that can be resolved by Nsp13 helicase in a unique manner with respect to nucleotide dependence.Nucleic acids research · 2025Article
- Spontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates.Nature communications · 2025Article
- Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2.Journal of the American Chemical Society · 2024Article
- Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses.RNA (New York, N.Y.) · 2024Article
- NMR characterization and ligand binding site of the stem-loop 2 motif from the Delta variant of SARS-CoV-2.RNA (New York, N.Y.) · 2024Article
- Large-scale analysis of small molecule-RNA interactions using multiplexed RNA structure libraries.Communications chemistry · 2024Article
- Article
- Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Exploring the conformational dynamics of the SARS-CoV-2 SL4 hairpin by combining optical tweezers and base analogues.Nanoscale · 2024Article
- RNA target highlights in CASP15: Evaluation of predicted models by structure providers.Proteins · 2023Article
- Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses.bioRxiv : the preprint server for biology · 2023Article
- Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics.Nucleic acids research · 2023Article
- High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR.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
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Authors and funding
10 authors at 4 institutions in 1 country.
Funding
Abstract
The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta's FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5' UTR; the reverse complement of the 5' UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3' UTR. For eleven of these elements (the stems in SL1-8, reverse complement of SL1-4, FSE, s2m and 3' UTR pseudoknot), modeling convergence supports the accuracy of predicted low energy states; subsequent cryo-EM characterization of the FSE confirms modeling accuracy. To aid efforts to discover small molecule RNA binders guided by computational models, we provide a second set of similarly prepared models for RNA riboswitches that bind small molecules. Both datasets ('FARFAR2-SARS-CoV-2', https://github.com/DasLab/FARFAR2-SARS-CoV-2; and 'FARFAR2-Apo-Riboswitch', at https://github.com/DasLab/FARFAR2-Apo-Riboswitch') include up to 400 models for each RNA element, which may facilitate drug discovery approaches targeting dynamic ensembles of RNA molecules.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.