ArticleJournal of structural biology2015
Directly reconstructing principal components of heterogeneous particles from cryo-EM images.
Article in Journal of structural biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Heterogeneous reconstruction algorithms for cryoEM achieve limited particle classification accuracy on real benchmark datasets.bioRxiv : the preprint server for biology · 2026Article
- Cryo-EM heterogeneity analysis using regularized covariance estimation and kernel regression.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- CryoSTAR: leveraging structural priors and constraints for cryo-EM heterogeneous reconstruction.Nature methods · 2024Article
- Cryo-EM Heterogeneity Analysis using Regularized Covariance Estimation and Kernel Regression.bioRxiv : the preprint server for biology · 2024Article
- MDSPACE and MDTOMO Software for Extracting Continuous Conformational Landscapes from Datasets of Single Particle Images and Subtomograms Based on Molecular Dynamics Simulations: Latest Developments in ContinuousFlex Software Package.International journal of molecular sciences · 2023Article
- KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion.Nature structural & molecular biology · 2023Article
- Novel Artificial Intelligence-Based Approaches for Ab Initio Structure Determination and Atomic Model Building for Cryo-Electron Microscopy.Micromachines · 2023Review
- MDTOMO method for continuous conformational variability analysis in cryo electron subtomograms based on molecular dynamics simulations.Scientific reports · 2023Article
- 3DFlex: determining structure and motion of flexible proteins from cryo-EM.Nature methods · 2023Article
- Methods for Cryo-EM Single Particle Reconstruction of Macromolecules Having Continuous Heterogeneity.Journal of molecular biology · 2023Review
- Exploring the Structural Variability of Dynamic Biological Complexes by Single-Particle Cryo-Electron Microscopy.Micromachines · 2022Review
- Amortized Inference for Heterogeneous Reconstruction in Cryo-EM.Advances in neural information processing systems · 2022Article
- Emerging Themes in CryoEM─Single Particle Analysis Image Processing.Chemical reviews · 2022Review
- Artificial Intelligence in Cryo-Electron Microscopy.Life (Basel, Switzerland) · 2022Review
- Visualizing Conformational Space of Functional Biomolecular Complexes by Deep Manifold Learning.International journal of molecular sciences · 2022Article
- Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity.Biomolecules · 2022Review
- Catalytic trajectory of a dimeric nonribosomal peptide synthetase subunit with an inserted epimerase domain.Nature communications · 2022Article
- DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images.Frontiers in molecular biosciences · 2022Article
- Article
- A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments.Scientific reports · 2021Article
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Authors and funding
5 authors.
Funding
Abstract
Structural heterogeneity of particles can be investigated by their three-dimensional principal components. This paper addresses the question of whether, and with what algorithm, the three-dimensional principal components can be directly recovered from cryo-EM images. The first part of the paper extends the Fourier slice theorem to covariance functions showing that the three-dimensional covariance, and hence the principal components, of a heterogeneous particle can indeed be recovered from two-dimensional cryo-EM images. The second part of the paper proposes a practical algorithm for reconstructing the principal components directly from cryo-EM images without the intermediate step of calculating covariances. This algorithm is based on maximizing the posterior likelihood using the Expectation-Maximization algorithm. The last part of the paper applies this algorithm to simulated data and to two real cryo-EM data sets: a data set of the 70S ribosome with and without Elongation Factor-G (EF-G), and a data set of the influenza virus RNA dependent RNA Polymerase (RdRP). The first principal component of the 70S ribosome data set reveals the expected conformational changes of the ribosome as the EF-G binds and unbinds. The first principal component of the RdRP data set reveals a conformational change in the two dimers of the RdRP.
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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.