ArticleNature communications2023
Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Digital twin of biomacromolecular thermodynamics in cryo-EM data.Communications chemistry · 2026Article
- Crossed laser phase plates for transmission electron microscopy.Nature communications · 2026Article
- Curvy Surface Reconstruction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Comparing cryo-EM methods and molecular dynamics simulation to investigate heterogeneity in ligand-bound TRPV1.Nature communications · 2025Article
- Cryo-electron microscopy ensemble optimization using individual particles and physical constraints.bioRxiv : the preprint server for biology · 2025Article
- The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge.bioRxiv : the preprint server for biology · 2025Article
- Deciphering conformational dynamics in AFM data using fast nonlinear NMA and FFT-based search with AFMFit.Communications biology · 2025Article
- CryoDRGN-AI: neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets.Nature methods · 2025Article
- Amortized template matching of molecular conformations from cryoelectron microscopy images using simulation-based inference.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Single-particle cryogenic electron microscopy structure determination for membrane proteins.Current opinion in structural biology · 2025Review
- CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features.Bioinformatics (Oxford, England) · 2025Article
- InstaMap: instant-NGP for cryo-EM density maps.Acta crystallographica. Section D, Structural biology · 2025Article
- 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
- A new statistical metric for robust target detection in cryo-EM using 2D template matching.IUCrJ · 2025Article
- Transient interactions between the fuzzy coat and the cross-β core of brain-derived Aβ42 filaments.Science advances · 2025Article
- CryoSTAR: leveraging structural priors and constraints for cryo-EM heterogeneous reconstruction.Nature methods · 2024Article
- DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images.Nature methods · 2024Article
- Cryo-EM Heterogeneity Analysis using Regularized Covariance Estimation and Kernel Regression.bioRxiv : the preprint server for biology · 2024Article
- CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM.Communications biology · 2024Article
- Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information.Nature communications · 2024Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
The new developments in Cryo-EM Single Particle Analysis are helping us to understand how the macromolecular structure and function meet to drive biological processes. By capturing many states at the particle level, it is possible to address how macromolecules explore different conformations, information that is classically extracted through 3D classification. However, the limitations of classical approaches prevent us from fully understanding the complete conformational landscape due to the reduced number of discrete states accurately reconstructed. To characterize the whole structural spectrum of a macromolecule, we propose an extension of our Zernike3D approach, able to extract per-image continuous flexibility information directly from a particle dataset. Also, our method can be seamlessly applied to images, maps or atomic models, opening integrative possibilities. Furthermore, we introduce the ZART reconstruction algorithm, which considers the Zernike3D deformation fields to revert particle conformational changes during the reconstruction process, thus minimizing the blurring induced by molecular motions.
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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.