ArticleNature communications2024
Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The trial behind it
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Who cites it
7 citing papers in PubMed.
- Computational Approaches for Protein-DNA/RNA Complex Modeling for Cryo-EM Maps.Current protocols · 2026Article
- ChironRNA: Steric Clashes Resolution in RNA Structures via E(3)-Equivariant Diffusion.bioRxiv : the preprint server for biology · 2026Article
- EMProt improves structure determination from cryo-EM maps.Nature structural & molecular biology · 2026Article
- Integrated experimental and AI innovations for RNA structure determination.Nature biotechnology · 2026Review
- AI meets RNA: revolutionizing structure prediction.Science China. Life sciences · 2025Article
- DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation.Nucleic acids research · 2025Article
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Cryo-electron microscopy (cryo-EM) is one of the most powerful experimental methods for macromolecular structure determination. However, accurate DNA/RNA structure modeling from cryo-EM maps is still challenging especially for protein-DNA/RNA or multi-chain DNA/RNA complexes. Here we propose a deep learning-based method for accurate de novo structure determination of DNA/RNA from cryo-EM maps at <5 Å resolutions, which is referred to as EM2NA. EM2NA is extensively evaluated on a diverse test set of 50 experimental maps at 2.0-5.0 Å resolutions, and compared with state-of-the-art methods including CryoREAD, ModelAngelo, and phenix.map_to_model. On average, EM2NA achieves a residue coverage of 83.15%, C4' RMSD of 1.06 Å, and sequence recall of 46.86%, which outperforms the existing methods. Moreover, EM2NA is applied to build the DNA/RNA structures with 10 to 5347 nt from an EMDB-wide data set of 263 unmodeled raw maps, demonstrating its ability in the blind model building of DNA/RNA from cryo-EM maps. EM2NA is fast and can normally build a DNA/RNA structure of <500 nt within 10 minutes.
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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.