ArticleNature methods2018
De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 65 citations in OpenAlex.
- A large-scale cryo-EM RNA motif dataset and benchmark for machine learning-based structure modeling.Computational biology and chemistry · 2026Article
- Base modifications shift tertiary structure and activity in synthetic RNA origami and a natural ribozyme.Nature communications · 2026Article
- A Large-Scale Cryo-EM RNA Motif Dataset and Benchmark for Machine Learning-Based Structure Modeling.bioRxiv : the preprint server for biology · 2026Article
- Structures of nucleotide-bound human telomerase at several steps of its telomeric DNA repeat addition cycle.Nature communications · 2026Article
- Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization.Science (New York, N.Y.) · 2025Article
- DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation.Nucleic acids research · 2025Article
- Article
- Structures of a natural circularly permuted group II intron reveal mechanisms of branching and backsplicing.Nature structural & molecular biology · 2025Article
- Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations.Nature communications · 2025Article
- Tick-borne flavivirus exoribonuclease-resistant RNAs contain a double loop structure.Nature communications · 2025Article
- All-atom RNA structure determination from cryo-EM maps.Nature biotechnology · 2025Article
- Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps.Nature communications · 2024Article
- Structural basis of Acinetobacter type IV pili targeting by an RNA virus.Nature communications · 2024Article
- A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM.Nucleic acids research · 2023Article
- RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli-Pepper aptamer FRET pair.Nucleic acids research · 2023Article
- Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.RNA (New York, N.Y.) · 2023Article
- Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM.Nature communications · 2023Article
- Advances and opportunities in RNA structure experimental determination and computational modeling.Nature methods · 2022Review
- Topological crossing in the misfoldedProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Three-dimensional structure-guided evolution of a ribosome with tethered subunits.Nature chemical biology · 2022Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
Increasingly, cryo-electron microscopy (cryo-EM) is used to determine the structures of RNA-protein assemblies, but nearly all maps determined with this method have biologically important regions where the local resolution does not permit RNA coordinate tracing. To address these omissions, we present de novo ribonucleoprotein modeling in real space through assembly of fragments together with experimental density in Rosetta (DRRAFTER). We show that DRRAFTER recovers near-native models for a diverse benchmark set of RNA-protein complexes including the spliceosome, mitochondrial ribosome, and CRISPR-Cas9-sgRNA complexes; rigorous blind tests include yeast U1 snRNP and spliceosomal P complex maps. Additionally, to aid in model interpretation, we present a method for reliable in situ estimation of DRRAFTER model accuracy. Finally, we apply DRRAFTER to recently determined maps of telomerase, the HIV-1 reverse transcriptase initiation complex, and the packaged MS2 genome, demonstrating the acceleration of accurate model building in challenging cases.
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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.