ArticlePLoS computational biology2024
Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- From possibility to precision in macromolecular ensemble prediction.Nature methods · 2026Article
- Time-resolved x-ray solution scattering from detergent solubilized visual rhodopsin.Biophysical journal · 2026Article
- Making PLUMED Fly: A Tutorial on Optimizing Performance.The journal of physical chemistry. B · 2026Article
- Atomic resolution ensembles of intrinsically disordered proteins with Alphafold.Nature communications · 2026Article
- Article
- Cryo-electron microscopy ensemble optimization using individual particles and physical constraints.bioRxiv : the preprint server for biology · 2025Article
- Blind prediction of complex water and ion ensembles around RNA in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity.bioRxiv : the preprint server for biology · 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
- An easy-to-use three-dimensional protein-structure-prediction online platform "DPL3D" based on deep learning algorithms.Current research in structural biology · 2025Article
- Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations.Nature communications · 2025Article
- Advances in uncovering the mechanisms of macromolecular conformational entropy.Nature chemical biology · 2025Review
- PLUMED Tutorials: A collaborative, community-driven learning ecosystem.The Journal of chemical physics · 2025Article
- Frontiers in integrative structural modeling of macromolecular assemblies.QRB discovery · 2025Review
- Data Science for Integrated Dynamic Structural Biology-the 21st IUPAB Congress session summary commentary.Biophysical reviews · 2024Article
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4 authors.
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Abstract
Converting cryo-electron microscopy (cryo-EM) data into high-quality structural models is a challenging problem of outstanding importance. Current refinement methods often generate unbalanced models in which physico-chemical quality is sacrificed for excellent fit to the data. Furthermore, these techniques struggle to represent the conformational heterogeneity averaged out in low-resolution regions of density maps. Here we introduce EMMIVox, a Bayesian inference approach to determine single-structure models as well as structural ensembles from cryo-EM maps. EMMIVox automatically balances experimental information with accurate physico-chemical models of the system and the surrounding environment, including waters, lipids, and ions. Explicit treatment of data correlation and noise as well as inference of accurate B-factors enable determination of structural models and ensembles with both excellent fit to the data and high stereochemical quality, thus outperforming state-of-the-art refinement techniques. EMMIVox represents a flexible approach to determine high-quality structural models that will contribute to advancing our understanding of the molecular mechanisms underlying biological functions.
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