ArticleActa crystallographica. Section D, Biological crystallography2012
RCrane: semi-automated RNA model building.
Article in Acta crystallographica. Section D, Biological crystallography, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters.PLoS computational biology · 2026Article
- ChironRNA: Steric Clashes Resolution in RNA Structures via E(3)-Equivariant Diffusion.bioRxiv : the preprint server for biology · 2026Article
- Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets.RNA (New York, N.Y.) · 2025Article
- Scaffold-enabled high-resolution cryo-EM structure determination of RNA.Nature communications · 2025Article
- Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps.Nature communications · 2024Article
- Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast.RNA (New York, N.Y.) · 2024Article
- Scaffold-enabled high-resolution cryo-EM structure determination of RNA.bioRxiv : the preprint server for biology · 2024Article
- Structural basis of branching during RNA splicing.Nature structural & molecular biology · 2024Article
- CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning.Nature methods · 2023Article
- DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.Nucleic acids research · 2023Article
- The dynamic architecture of Map1- and NatB-ribosome complexes coordinates the sequential modifications of nascent polypeptide chains.PLoS biology · 2023Article
- Structural transitions during the cooperative assembly of baculovirus single-stranded DNA-binding protein on ssDNA.Nucleic acids research · 2022Article
- Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot.RNA (New York, N.Y.) · 2022Article
- Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer.Nucleic acids research · 2020Article
- Current developments in Coot for macromolecular model building of Electron Cryo-microscopy and Crystallographic Data.Protein science : a publication of the Protein Society · 2020Article
- Structural and biophysical properties of RIG-I bound to dsRNA with G-U wobble base pairs.RNA biology · 2020Article
- Integrative structural biology studies of HIV-1 reverse transcriptase binding to a high-affinity DNA aptamer.Current research in structural biology · 2020Article
- How far are we from automatic crystal structure solution via molecular-replacement techniques?Acta crystallographica. Section D, Structural biology · 2020Article
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2 authors.
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Abstract
RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.
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