ArticleNature biotechnology2025
All-atom RNA structure determination from cryo-EM maps.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- The trRosettaRNA server for RNA structure prediction.Nature protocols · 2026Review
- Computational Approaches for Protein-DNA/RNA Complex Modeling for Cryo-EM Maps.Current protocols · 2026Article
- EMReady2: improvement of cryo-EM and cryo-ET maps by local quality-aware deep learning with Mamba.Nature communications · 2026Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- Integrated experimental and AI innovations for RNA structure determination.Nature biotechnology · 2026Review
- EMProt improves structure determination from cryo-EM maps.Nature structural & molecular biology · 2026Article
- CryoAtom improves model building for cryo-EM.Nature structural & molecular biology · 2026Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- Quantifying the liquid-liquid transition in cold water/glycerol mixtures by intermolecular hyperfine relaxation-induced dipolar modulation enhancement (ih-RIDME).Physical chemistry chemical physics : PCCP · 2025Article
- RBMX2 linkseLife · 2025Article
- Artificial intelligence in bioinformatics: a survey.Briefings in bioinformatics · 2025Review
- Structural insights into higher-order natural RNA-only multimers.Nature structural & molecular biology · 2025Article
- Transcriptome-wide RNA accessibility mapping reveals structured RNA elements and pervasive conformational rearrangements under stress.bioRxiv : the preprint server for biology · 2025Article
- Advancing structure modeling from cryo-EM maps with deep learning.Biochemical Society transactions · 2025Review
- Gut microbiota dysbiosis induces neuroinflammation in major depressive disorders: mechanisms targeting the gut-brain axis.Frontiers in psychiatry · 2025Review
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- Ligand identification in CryoEM and X-ray maps using deep learning.Bioinformatics (Oxford, England) · 2024Article
- Ligand Identification in CryoEM and X-ray Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2024Article
- AI-integrated network for RNA complex structure and dynamic prediction.Biophysics reviews · 2024Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Many methods exist for determining protein structures from cryogenic electron microscopy maps, but this remains challenging for RNA structures. Here we developed EMRNA, a method for accurate, automated determination of full-length all-atom RNA structures from cryogenic electron microscopy maps. EMRNA integrates deep learning-based detection of nucleotides, three-dimensional backbone tracing and scoring with consideration of sequence and secondary structure information, and full-atom construction of the RNA structure. We validated EMRNA on 140 diverse RNA maps ranging from 37 to 423 nt at 2.0-6.0 Å resolutions, and compared EMRNA with auto-DRRAFTER, phenix.map_to_model and CryoREAD on a set of 71 cases. EMRNA achieves a median accuracy of 2.36 Å root mean square deviation and 0.86 TM-score for full-length RNA structures, compared with 6.66 Å and 0.58 for auto-DRRAFTER. EMRNA also obtains a high residue coverage and sequence match of 93.30% and 95.30% in the built models, compared with 58.20% and 42.20% for phenix.map_to_model and 56.45% and 52.3% for CryoREAD. EMRNA is fast and can build an RNA structure of 100 nt within 3 min.
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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.