ArticleBiophysical journal2022
DeepTracer-ID: De novo protein identification from cryo-EM maps.
Article in Biophysical journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- 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
- Advances in Crystallography and Cryo-Electron Microscopy for the Study of Membrane Proteins.Advances in experimental medicine and biology · 2026Review
- From CASP13 to the Nobel Prize: DeepMind's AlphaFold Journey in Revolutionizing Protein Structure Prediction and Beyond.Current protein & peptide science · 2026Review
- 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
- CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes.Structure (London, England : 1993) · 2025Article
- A family of tubular pili from harmful algal bloom forming cyanobacterium Microcystis aeruginosa.Nature communications · 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
- Finding antibodies in cryo-EM maps with CrAI.Bioinformatics (Oxford, England) · 2025Article
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- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- Frontiers in integrative structural modeling of macromolecular assemblies.QRB discovery · 2025Review
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- Two distinct archaeal type IV pili structures formed by proteins with identical sequence.Nature communications · 2024Article
- Structural determination and modeling of ciliary microtubules.Acta crystallographica. Section D, Structural biology · 2024Review
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- An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano.Nature communications · 2024Article
- Cryo-EM of a heterogeneous biochemical fraction elucidates multiple protein complexes from a multicellular thermophilic eukaryote.Journal of structural biology: X · 2023Article
- Automated model building and protein identification in cryo-EM maps.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
The recent revolution in cryo-electron microscopy (cryo-EM) has made it possible to determine macromolecular structures directly from cell extracts. However, identifying the correct protein from the cryo-EM map is still challenging and often needs additional sequence information from other techniques, such as tandem mass spectrometry and/or bioinformatics. Here, we present DeepTracer-ID, a server-based approach to identify the candidate protein in a user-provided organism de novo from a cryo-EM map, without the need for additional information. Our method first uses DeepTracer to generate a protein backbone model that best represents the cryo-EM map, and this model is then searched against the library of AlphaFold2 predictions for all proteins in the given organism. This method is highly accurate and robust for high-resolution cryo-EM maps: in all 13 experimental maps tested blindly, DeepTracer-ID identified the correct proteins as the top candidates. Eight of the maps were of known structures, while the other five unpublished maps were validated by prior protein annotation and careful inspection of the model refined into the map. The program also showed promising results for both homomeric and heteromeric protein complexes. This platform is possible because of the recent breakthroughs in large-scale three-dimensional protein structure prediction.
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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.