ArticleNature communications2024
Cryo-EM structure and B-factor refinement with ensemble representation.
Article in Nature communications, 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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Who cites it
16 citing papers in PubMed.
- A GABARAP-PtdIns3K-C1 positive feedback loop at the heart of the phagophore nucleation.Nature communications · 2026Article
- Pinpointing Protein Crystal Structures over a Broad Temperature Range Using Hydrophobic Protection.ACS omega · 2026Article
- Structure of a pH-sensitive pentameric ligand-gated ion channel from the Sarcoptes scabies mite.Nature communications · 2026Article
- Cryo-EM Analysis in CASP16.Proteins · 2026Article
- Cryo-electron microscopy ensemble optimization using individual particles and physical constraints.bioRxiv : the preprint server for biology · 2025Article
- Hemoglobin receptor redundancy inJournal of structural biology: X · 2025Article
- Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.Nature communications · 2025Article
- Article
- Temperature-Resolved Crystallography Reveals Rigid-Body Dominance over Local Flexibility in B‑Factors.ACS omega · 2025Article
- Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps.Acta crystallographica. Section D, Structural biology · 2025Article
- Advances in uncovering the mechanisms of macromolecular conformational entropy.Nature chemical biology · 2025Review
- When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines.Computational and structural biotechnology journal · 2025Article
- Frontiers in integrative structural modeling of macromolecular assemblies.QRB discovery · 2025Review
- How structural biology has changed our understanding of icosahedral viruses.Journal of virology · 2024Review
- Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference.PLoS computational biology · 2024Article
- CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps.Proteins · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Cryo-EM experiments produce images of macromolecular assemblies that are combined to produce three-dimensional density maps. Typically, atomic models of the constituent molecules are fitted into these maps, followed by a density-guided refinement. We introduce TEMPy-ReFF, a method for atomic structure refinement in cryo-EM density maps. Our method represents atomic positions as components of a Gaussian mixture model, utilising their variances as B-factors, which are used to derive an ensemble description. Extensively tested on a substantial dataset of 229 cryo-EM maps from EMDB ranging in resolution from 2.1-4.9 Å with corresponding PDB and CERES atomic models, our results demonstrate that TEMPy-ReFF ensembles provide a superior representation of cryo-EM maps. On a single-model basis, it performs similarly to the CERES re-refinement protocol, although there are cases where it provides a better fit to the map. Furthermore, our method enables the creation of composite maps free of boundary artefacts. TEMPy-ReFF is useful for better interpretation of flexible structures, such as those involving RNA, DNA or ligands.
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