ArticleBioinformatics (Oxford, England)2023
RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- The RNA-Puzzles Assessments of RNA-Only Targets in CASP16.Proteins · 2026Article
- Evolution of the RNA alternative decayRNA biology · 2025Article
- A conserved viral RNA fold enables nuclease resistance across kingdoms of life.Nucleic acids research · 2025Article
- Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering.Structure (London, England : 1993) · 2025Article
- Predicting RNA structure and dynamics with deep learning and solution scattering.Biophysical journal · 2025Article
- Predicting RNA Structure and Dynamics with Deep Learning and Solution Scattering.bioRxiv : the preprint server for biology · 2024Article
- The pseudoknot structure of a viral RNA reveals a conserved mechanism for programmed exoribonuclease resistance.bioRxiv : the preprint server for biology · 2024Article
- Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering.bioRxiv : the preprint server for biology · 2024Article
- Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.Nucleic acids research · 2024Article
- Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.Nucleic acids research · 2024Article
- Hierarchical Assembly of Single-Stranded RNA.Journal of chemical theory and computation · 2024Article
- NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin.Nucleic acids research · 2022Article
- Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models.Viruses · 2021Article
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5 authors.
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Abstract
summaryStructure determination is a key step in the functional characterization of many non-coding RNA molecules. High-resolution RNA 3D structure determination efforts, however, are not keeping up with the pace of discovery of new non-coding RNA sequences. This increases the importance of computational approaches and low-resolution experimental data, such as from the small-angle X-ray scattering experiments. We present RNA Masonry, a computer program and a web service for a fully automated modeling of RNA 3D structures. It assemblies RNA fragments into geometrically plausible models that meet user-provided secondary structure constraints, restraints on tertiary contacts, and small-angle X-ray scattering data. We illustrate the method description with detailed benchmarks and its application to structural studies of viral RNAs with SAXS restraints. AVAILABILITY AND IMPLEMENTATION: The program web server is available at http://iimcb.genesilico.pl/rnamasonry. The source code is available at https://gitlab.com/gchojnowski/rnamasonry.
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