ArticleBriefings in bioinformatics2023
Fast and automated protein-DNA/RNA macromolecular complex modeling from cryo-EM maps.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- A large-scale cryo-EM RNA motif dataset and benchmark for machine learning-based structure modeling.Computational biology and chemistry · 2026Article
- Computational Approaches for Protein-DNA/RNA Complex Modeling for Cryo-EM Maps.Current protocols · 2026Article
- A Large-Scale Cryo-EM RNA Motif Dataset and Benchmark for Machine Learning-Based Structure Modeling.bioRxiv : the preprint server for biology · 2026Article
- Integrated experimental and AI innovations for RNA structure determination.Nature biotechnology · 2026Review
- Structural basis of outer membrane biogenesis by the TamAB translocase.Nature communications · 2026Article
- Structures of Helicobacter pylori C-terminal protease CtpA reveal a new mode of self-contained proteolytic processing.Communications biology · 2025Article
- Impurities in amyloid studies: The power of automated model building within a cautionary tale for structural biologists.Protein science : a publication of the Protein Society · 2025Article
- DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation.Nucleic acids research · 2025Article
- A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps.Briefings in bioinformatics · 2025Article
- RNA sample optimization for cryo-EM analysis.Nature protocols · 2025Review
- Advancing structure modeling from cryo-EM maps with deep learning.Biochemical Society transactions · 2025Review
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- 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
- Article
- Structural basis of antiphage immunity generated by a prokaryotic Argonaute-associated SPARSA system.Nature communications · 2024Article
- Automated model building and protein identification in cryo-EM maps.bioRxiv : the preprint server for biology · 2023Article
- Novel Artificial Intelligence-Based Approaches for Ab Initio Structure Determination and Atomic Model Building for Cryo-Electron Microscopy.Micromachines · 2023Review
- DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.Nucleic acids research · 2023Article
Corrections and comments
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7 authors.
Funding
Abstract
Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb potential map. The structural information of these macromolecular complexes forms the foundation for understanding the molecular mechanism including many human diseases. However, the model building of large macromolecular complexes is often difficult and time-consuming. We recently developed DeepTracer-2.0, an artificial-intelligence-based pipeline that can build amino acid and nucleic acid backbones from a single cryo-EM map, and even predict the best-fitting residues according to the density of side chains. The experiments showed improved accuracy and efficiency when benchmarking the performance on independent experimental maps of protein-DNA/RNA complexes and demonstrated the promising future of macromolecular modeling from cryo-EM maps. Our method and pipeline could benefit researchers worldwide who work in molecular biomedicine and drug discovery, and substantially increase the throughput of the cryo-EM model building. The pipeline has been integrated into the web portal https://deeptracer.uw.edu/.
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