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OPUS-TOMO: Towards Resolving Dynamics and Compositional Heterogeneities of Biomolecules with Cryo-Electron Tomography

https://doi.org/10.1101/2024.06.30.601442
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The promise and the challenges of cryo‐electron tomography
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UCSF ChimeraX: Meeting modern challenges in visualization and analysis
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Computer Visualization of Three-Dimensional Image Data Using IMOD
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Cryo-Electron Tomography and Subtomogram Averaging
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Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy
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CTF determination and correction for low dose tomographic tilt series
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PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis
inferredcites →https://doi.org/10.1016/j.jsb.2016.07.011openalex-snapshot
Automated tilt series alignment and tomographic reconstruction in IMOD
inferredcites →https://doi.org/10.1016/j.jsb.2018.12.008openalex-snapshot
Rapid tilt-series acquisition for electron cryotomography
inferredcites →https://doi.org/10.1016/j.jsb.2019.08.006openalex-snapshot
Improved applicability and robustness of fast cryo-electron tomography data acquisition
inferredcites →https://doi.org/10.1016/j.jsb.2021.107778openalex-snapshot
TomoAlign: A novel approach to correcting sample motion and 3D CTF in CryoET
inferredcites →https://doi.org/10.1016/j.jsb.2023.108057openalex-snapshot
Accurate, automatic determination of astigmatism and phase with Ctfplotter in IMOD
inferredcites →https://doi.org/10.1016/j.molcel.2025.11.029openalex-snapshot
Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
inferredcites →https://doi.org/10.1016/j.sbi.2019.03.018openalex-snapshot
Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging
inferredcites →https://doi.org/10.1016/j.sbi.2019.05.021openalex-snapshot
Advances in cryo-electron tomography and subtomogram averaging and classification
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Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes
inferredcites →https://doi.org/10.1016/j.str.2015.06.026openalex-snapshot
Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging
inferredcites →https://doi.org/10.1016/j.tcb.2016.08.006openalex-snapshot
Cryo-Electron Tomography: Can it Reveal the Molecular Sociology of Cells in Atomic Detail?
inferredcites →https://doi.org/10.1016/j.yjsbx.2022.100068openalex-snapshot
AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction
inferredcites →https://doi.org/10.1016/s0076-6879(10)83011-3openalex-snapshot
Visual Proteomics
inferredcites →https://doi.org/10.1016/s0969-2126(02)00789-xopenalex-snapshot
A Dynamic Analysis of the Rotation Mechanism for Conformational Change in F1-ATPase
inferredcites →https://doi.org/10.1017/s1431927621006176openalex-snapshot
Continuous heterogeneity analysis of CryoEM images through Zernike polynomials and spherical harmonics
inferredcites →https://doi.org/10.1017/s1431927622005074openalex-snapshot
3D Flexible Refinement: Structure and Motion of Flexible Proteins from Cryo-EM
inferredcites →https://doi.org/10.1038/nature05126openalex-snapshot
Structure of eEF3 and the mechanism of transfer RNA release from the E-site
inferredcites →https://doi.org/10.1038/nature06523openalex-snapshot
The molecular sociology of the cell
inferredcites →https://doi.org/10.1038/nprot.2016.124openalex-snapshot
Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION
inferredcites →https://doi.org/10.1038/s41467-020-14603-7openalex-snapshot
MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments
inferredcites →https://doi.org/10.1038/s41467-023-35791-yopenalex-snapshot
Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials
inferredcites →https://doi.org/10.1038/s41586-021-03819-2openalex-snapshot
Highly accurate protein structure prediction with AlphaFold
inferredcites →https://doi.org/10.1038/s41586-021-04131-9openalex-snapshot
Accuracy mechanism of eukaryotic ribosome translocation
inferredcites →https://doi.org/10.1038/s41586-022-05255-2openalex-snapshot
Visualizing translation dynamics at atomic detail inside a bacterial cell
inferredcites →https://doi.org/10.1038/s41586-024-07508-8openalex-snapshot
Structural mechanism of angiogenin activation by the ribosome
inferredcites →https://doi.org/10.1038/s41592-018-0167-zopenalex-snapshot
emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging
inferredcites →https://doi.org/10.1038/s41592-019-0580-yopenalex-snapshot
Real-time cryo-electron microscopy data preprocessing with Warp
inferredcites →https://doi.org/10.1038/s41592-019-0675-5openalex-snapshot
Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms
inferredcites →https://doi.org/10.1038/s41592-020-01049-4openalex-snapshot
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks
inferredcites →https://doi.org/10.1038/s41592-020-01054-7openalex-snapshot
Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells
inferredcites →https://doi.org/10.1038/s41592-022-01746-2openalex-snapshot
Convolutional networks for supervised mining of molecular patterns within cellular context
inferredcites →https://doi.org/10.1038/s41592-023-02031-6openalex-snapshot
OPUS-DSD: deep structural disentanglement for cryo-EM single-particle analysis
inferredcites →https://doi.org/10.1038/s41592-023-02045-0openalex-snapshot
nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography
inferredcites →https://doi.org/10.1038/s41592-024-02210-zopenalex-snapshot
Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN
inferredcites →https://doi.org/10.1042/bcj20200715openalex-snapshot
Current data processing strategies for cryo-electron tomography and subtomogram averaging
inferredcites →https://doi.org/10.1073/pnas.0805827105openalex-snapshot
Inhibition of the fungal fatty acid synthase type I multienzyme complex
inferredcites →https://doi.org/10.1073/pnas.0811370106openalex-snapshot
Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis
inferredcites →https://doi.org/10.1073/pnas.0913547107openalex-snapshot
Direct structural insight into the substrate-shuttling mechanism of yeast fatty acid synthase by electron cryomicroscopy
inferredcites →https://doi.org/10.1073/pnas.1009999107openalex-snapshot
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution
inferredcites →https://doi.org/10.1073/pnas.1501775112openalex-snapshot
Cryo-EM structure of the tetracycline resistance protein TetM in complex with a translating ribosome at 3.9-Å resolution
inferredcites →https://doi.org/10.1073/pnas.2013756118openalex-snapshot
Sparseness and Smoothness Regularized Imaging for improving the resolution of Cryo-EM single-particle reconstruction
inferredcites →https://doi.org/10.1073/pnas.230282097openalex-snapshot
Toward detecting and identifying macromolecules in a cellular context: Template matching applied to electron tomograms
inferredcites →https://doi.org/10.1093/nar/gkab1061openalex-snapshot
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
inferredcites →https://doi.org/10.1101/2023.08.18.553799openalex-snapshot
Deep reconstructing generative networks for visualizing dynamic biomolecules inside cells
inferredcites →https://doi.org/10.1107/s010876739101067xopenalex-snapshot
The crystallographic information file (CIF): a new standard archive file for crystallography
inferredcites →https://doi.org/10.1109/tit.1982.1056489openalex-snapshot
Least squares quantization in PCM
inferredcites →https://doi.org/10.1126/science.aaw9128openalex-snapshot
Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F 1 -F o coupling
inferredcites →https://doi.org/10.1126/science.abb3758openalex-snapshot
In-cell architecture of an actively transcribing-translating expressome
inferredcites →https://doi.org/10.1126/science.adp4640openalex-snapshot
In situ structure and rotary states of mitochondrial ATP synthase in whole Polytomella cells
inferredcites →https://doi.org/10.1242/jcs.060111openalex-snapshot
Visualizing cellular processes at the molecular level by cryo-electron tomography
inferredcites →https://doi.org/10.1261/rna.069260.118openalex-snapshot
High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition
inferredcites →https://doi.org/10.15252/embj.2020106449openalex-snapshot
Yeast translation elongation factor eEF3 promotes late stages of tRNA translocation
inferredcites →https://doi.org/10.21105/joss.00861openalex-snapshot
UMAP: Uniform Manifold Approximation and Projection
inferredcites →https://doi.org/10.3390/ijms241713375openalex-snapshot
Extensive Angular Sampling Enables the Sensitive Localization of Macromolecules in Electron Tomograms
inferredcites →https://doi.org/10.5281/zenodo.12631919openalex-snapshot
Results for "OPUS-ET: Resolving Compositional and Conformational Heterogeneities of Biomolecules in Cryo-Electron Tomography"
inferredcites →https://doi.org/10.5281/zenodo.13626516openalex-snapshot
source code for OPUS-ET
inferredcites →https://doi.org/10.7554/elife.36861openalex-snapshot
Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION
inferredcites →https://doi.org/10.7554/elife.52286openalex-snapshot
Fully automated, sequential focused ion beam milling for cryo-electron tomography
inferredcites →https://doi.org/10.7554/elife.70506openalex-snapshot
A modular platform for automated cryo-FIB workflows

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/pro.70679openalex-snapshot
CoCryoViS: Collaborative online cryo‐electron tomography visualization system
inferred← citeshttps://doi.org/10.1016/j.molcel.2025.11.029openalex-snapshot
Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
inferred← citeshttps://doi.org/10.1101/2024.09.24.614854openalex-snapshot
OPUS-DSD2: Disentangling Dynamics and Compositional Heterogeneity for Cryo-EM/ET
inferred← citeshttps://doi.org/10.64898/2025.12.19.695382openalex-snapshot
The In Situ Structure and Distribution of V-ATPase in C. elegans Apical Membrane Stacks
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