ArticleProceedings of the National Academy of Sciences of the United States of America2021
DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers.
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131 citing papers in PubMed.
- Convergence of cryo-electron microscopy and artificial intelligence in integrative structural biology: A critical review of advances, synergies, and implications for molecular biophysics and drug discovery.Journal of microscopy · 2026Review
- Distinct amyloid-β filament fold in individuals with APP Flemish mutation.Nature structural & molecular biology · 2026Article
- Structural basis of sex pheromone detection in aphids.Cell research · 2026Article
- Computational Approaches for Protein-DNA/RNA Complex Modeling for Cryo-EM Maps.Current protocols · 2026Article
- Artificial Intelligence for Discovery in Life Sciences.Bioconjugate chemistry · 2026Review
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- EMReady2: improvement of cryo-EM and cryo-ET maps by local quality-aware deep learning with Mamba.Nature communications · 2026Article
- Article
- ChironRNA: Steric Clashes Resolution in RNA Structures via E(3)-Equivariant Diffusion.bioRxiv : the preprint server for biology · 2026Article
- Discovery and cryoEM structure of FPM13, a periplasmic metalloprotein unique to Francisella.PLoS pathogens · 2026Article
- Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta.bioRxiv : the preprint server for biology · 2026Article
- Structure first - exploration and discovery with cryo-electron microscopy.Journal of cell science · 2026Review
- Cytochrome nanowires under electron microscopy.Emerging topics in life sciences · 2026Review
- CryoAtom improves model building for cryo-EM.Nature structural & molecular biology · 2026Article
- EMProt improves structure determination from cryo-EM maps.Nature structural & molecular biology · 2026Article
- A comprehensive foundation model for cryo-EM image processing.Nature methods · 2026Article
- Atomic models of the Toxoplasma cell invasion machinery.Nature structural & molecular biology · 2026Article
- Structure, identification, and characterization of the RibD-enolase complex in Francisella.Protein & cell · 2025Article
- Denoising and iterative phase recovery reveal low-occupancy populations in protein crystals.Communications biology · 2025Article
- Structures of Helicobacter pylori C-terminal protease CtpA reveal a new mode of self-contained proteolytic processing.Communications biology · 2025Article
71 more citing papers are in PubMed but not listed here.
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Abstract
Information about macromolecular structure of protein complexes and related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully automated deep learning-based method for fast de novo multichain protein complex structure determination from high-resolution cryoelectron microscopy (cryo-EM) maps. We applied DeepTracer on a previously published set of 476 raw experimental cryo-EM maps and compared the results with a current state of the art method. The residue coverage increased by over 30% using DeepTracer, and the rmsd value improved from 1.29 Å to 1.18 Å. Additionally, we applied DeepTracer on a set of 62 coronavirus-related cryo-EM maps, among them 10 with no deposited structure available in EMDataResource. We observed an average residue match of 84% with the deposited structures and an average rmsd of 0.93 Å. Additional tests with related methods further exemplify DeepTracer's competitive accuracy and efficiency of structure modeling. DeepTracer allows for exceptionally fast computations, making it possible to trace around 60,000 residues in 350 chains within only 2 h. The web service is globally accessible at https://deeptracer.uw.edu.
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