ArticlePLoS biology2021
Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo.
Article in PLoS biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Cryo-ET reveals distinct Gag lattice architectures in virus-like particles and immature HIV-1.Structure (London, England : 1993) · 2026Article
- Ultrastructural and atomic characterization of biofilm-associated extracellular filaments in Shewanella oneidensis MR-1.Nature communications · 2026Article
- Diel remodeling and cellular integration of the nitroplast.bioRxiv : the preprint server for biology · 2026Article
- Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.Acta crystallographica. Section D, Structural biology · 2026Article
- High-resolution analysis of the human T-cell leukemia virus capsid protein reveals insights into immature particle morphology.Nature communications · 2025Article
- Structural polymorphism of two-dimensional lattices assembled from baculoviral capsid proteins.Virologica Sinica · 2025Article
- Subnanometer-resolution Structural Determination of Hemagglutinin from Cryo-electron Tomography of Influenza Viruses.Journal of visualized experiments : JoVE · 2025Article
- Intracellular Ebola virus nucleocapsid assembly revealed by in situ cryo-electron tomography.Cell · 2024Article
- Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows.Acta crystallographica. Section D, Structural biology · 2024Article
- Blik is an extensible 3D visualisation tool for the annotation and analysis of cryo-electron tomography data.PLoS biology · 2024Article
- Accurate, automatic determination of astigmatism and phase with Ctfplotter in IMOD.Journal of structural biology · 2024Article
- The big chill: Growth ofQRB discovery · 2024Review
- Integrative Approaches to Study Virus Structures.Sub-cellular biochemistry · 2024Review
- TomoNet: A streamlined cryogenic electron tomography software pipeline with automatic particle picking on flexible lattices.Biological imaging · 2024Article
- Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR.Nature communications · 2023Article
- Correlative montage parallel array cryo-tomography for in situ structural cell biology.Nature methods · 2023Article
- HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation.Journal of molecular biology · 2023Article
- Computational Methods Toward Unbiased Pattern Mining and Structure Determination in Cryo-Electron Tomography Data.Journal of molecular biology · 2023Review
- In Situ Structure Determination of Bacterial Surface Nanomachines Using Cryo-Electron Tomography.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Computational methods forFrontiers in cellular and infection microbiology · 2023Review
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Subtomogram averaging (STA) is a powerful image processing technique in electron tomography used to determine the 3D structure of macromolecular complexes in their native environments. It is a fast growing technique with increasing importance in structural biology. The computational aspect of STA is very complex and depends on a large number of variables. We noticed a lack of detailed guides for STA processing. Also, current publications in this field often lack a documentation that is practical enough to reproduce the results with reasonable effort, which is necessary for the scientific community to grow. We therefore provide a complete, detailed, and fully reproducible processing protocol that covers all aspects of particle picking and particle alignment in STA. The command line-based workflow is fully based on the popular Dynamo software for STA. Within this workflow, we also demonstrate how large parts of the processing pipeline can be streamlined and automatized for increased throughput. This protocol is aimed at users on all levels. It can be used for training purposes, or it can serve as basis to design user-specific projects by taking advantage of the flexibility of Dynamo by modifying and expanding the given pipeline. The protocol is successfully validated using the Electron Microscopy Public Image Archive (EMPIAR) database entry 10164 from immature HIV-1 virus-like particles (VLPs) that describe a geometry often seen in electron tomography.
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