ArticleProceedings of the National Academy of Sciences of the United States of America2010
Semiautomated model building for RNA crystallography using a directed rotameric approach.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Exploring Conformational Transitions of Adenine RNA Dimer via Machine Learning Potentials.Journal of chemical theory and computation · 2026Article
- RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters.PLoS computational biology · 2026Article
- Lifetime of ground conformational state determines the activity of structured RNA.Nature chemical biology · 2025Article
- Scaffold-enabled high-resolution cryo-EM structure determination of RNA.Nature communications · 2025Article
- Scaffold-enabled high-resolution cryo-EM structure determination of RNA.bioRxiv : the preprint server for biology · 2024Article
- ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures.Molecules (Basel, Switzerland) · 2024Article
- Structural basis of branching during RNA splicing.Nature structural & molecular biology · 2024Article
- The pseudotorsional space of RNA.RNA (New York, N.Y.) · 2023Article
- Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product.Biochemistry · 2022Article
- AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.Bioinformatics (Oxford, England) · 2022Article
- Refinement of RNA Structures Using Amber Force Fields.Crystals · 2021Article
- RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures.Bioinformatics (Oxford, England) · 2021Article
- Structural basis for the second step of group II intron splicing.Nature communications · 2018Article
- De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes.Nature methods · 2018Article
- Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators.Cell chemical biology · 2018Article
- A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding.The Journal of biological chemistry · 2018Article
- 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase.Molecular cell · 2017Article
- Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme.Nature structural & molecular biology · 2017Article
- Structure determination of group II introns.Methods (San Diego, Calif.) · 2017Review
- Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme.Journal of the American Chemical Society · 2017Article
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2 authors.
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Abstract
Structured RNA molecules play essential roles in a variety of cellular processes; however, crystallographic studies of such RNA molecules present a large number of challenges. One notable complication arises from the low resolutions typical of RNA crystallography, which results in electron density maps that are imprecise and difficult to interpret. This problem is exacerbated by the lack of computational tools for RNA modeling, as many of the techniques commonly used in protein crystallography have no equivalents for RNA structure. This leads to difficulty and errors in the model building process, particularly in modeling of the RNA backbone, which is highly error prone due to the large number of variable torsion angles per nucleotide. To address this, we have developed a method for accurately building the RNA backbone into maps of intermediate or low resolution. This method is semiautomated, as it requires a crystallographer to first locate phosphates and bases in the electron density map. After this initial trace of the molecule, however, an accurate backbone structure can be built without further user intervention. To accomplish this, backbone conformers are first predicted using RNA pseudotorsions and the base-phosphate perpendicular distance. Detailed backbone coordinates are then calculated to conform both to the predicted conformer and to the previously located phosphates and bases. This technique is shown to produce accurate backbone structure even when starting from imprecise phosphate and base coordinates. A program implementing this methodology is currently available, and a plugin for the Coot model building program is under development.
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