ArticleViruses2021
Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models.
Article in Viruses, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Real-time medical images enhancement technique using Adaptive Histogram Equalization model.Scientific reports · 2026Article
- Challenges in simulating whole virus particles and how to fix them with the SIRAH force field.Biophysical reviews · 2025Review
- Unknotting RNA: A method to resolve computational artifacts.PLoS computational biology · 2025Article
- Review
- Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model.Macromolecular rapid communications · 2024Article
- Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.Nucleic acids research · 2024Article
- Knotted artifacts in predicted 3D RNA structures.PLoS computational biology · 2024Article
- Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa.Nature communications · 2023Article
- A multidisciplinary approach to the identification of the protein-RNA connectome in double-stranded RNA virus capsids.Nucleic acids research · 2023Article
- When 3D genome technology meets viral infection, including SARS-CoV-2.Journal of medical virology · 2022Review
- Single-chain models illustrate the 3D RNA folding shape during translation.Biophysical reports · 2022Article
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Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based on secondary structures from experimental techniques. Despite the amount of sampling involved in the folded and also unfolded RNA molecules, advanced microscope techniques can provide points of anchoring, which enhance our model to include interactions between capsid pentamers and RNA subdomains. To test our method, we tackle the satellite tobacco mosaic virus (STMV) genome, which has been widely studied by both experimental and computational communities. We provide not only a methodology to structurally analyze the tertiary conformations of the RNA genome inside capsids, but a flexible platform that allows the easy implementation of features/descriptors coming from both theoretical and experimental approaches.
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Registered trials
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