ArticleIEEE transactions on computational imaging2022
Recovery of Conformational Continuum From Single-Particle Cryo-EM Images: Optimization of ManifoldEM Informed by Ground Truth.
Article in IEEE transactions on computational imaging, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Digital twin of biomacromolecular thermodynamics in cryo-EM data.Communications chemistry · 2026Article
- Comparing cryo-EM methods and molecular dynamics simulation to investigate heterogeneity in ligand-bound TRPV1.Nature communications · 2025Article
- Molecular Insights into Macromolecules Structure, Function, and Regulation.International journal of molecular sciences · 2024Article
- Scaling up cryo-EM for biology and chemistry: The journey from niche technology to mainstream method.Structure (London, England : 1993) · 2023Review
- Novel Artificial Intelligence-Based Approaches for Ab Initio Structure Determination and Atomic Model Building for Cryo-Electron Microscopy.Micromachines · 2023Review
- Beyond ManifoldEM: geometric relationships between manifold embeddings of a continuum of 3D molecular structures and their 2D projections.Digital discovery · 2023Article
- Methods for Cryo-EM Single Particle Reconstruction of Macromolecules Having Continuous Heterogeneity.Journal of molecular biology · 2023Review
- Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models.Journal of molecular biology · 2023Article
- Energy landscapes from cryo-EM snapshots: a benchmarking study.Scientific reports · 2023Article
- Exploring the Structural Variability of Dynamic Biological Complexes by Single-Particle Cryo-Electron Microscopy.Micromachines · 2022Review
- Emerging Themes in CryoEM─Single Particle Analysis Image Processing.Chemical reviews · 2022Review
- The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.PLoS pathogens · 2022Article
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Authors and funding
5 authors.
Funding
Abstract
This work is based on the manifold-embedding approach to study biological molecules exhibiting continuous conformational changes. Previous work established a method-now termed ManifoldEM-capable of reconstructing 3D movies and accompanying free-energy landscapes from single-particle cryo-EM images of macromolecules exercising multiple conformational degrees of freedom. While ManifoldEM has proven its viability in several experimental studies, critical limitations and uncertainties have been found throughout its extended development and use. Guided by insights from studies with cryo-EM ground-truth data, simulated from atomic structures undergoing conformational changes, we have built a novel framework, ESPER, able to retrieve the free-energy landscape and respective 3D Coulomb potential maps for all states simulated. As shown by a direct comparison of ground truth vs. recovered maps, and analysis of experimental data from the 80S ribosome and ryanodine receptor, ESPER offers substantial improvements relative to the previous work.
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