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Cited by 11Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and DynamicsEnzyme Structure and Function

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Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks

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Chen, Muyuan·2025·Communications Biology
DOI 10.1038/s42003-025-08202-9PMC PMC12104439

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Abstract

Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores. This method makes it easier to interpret the movement of the protein complex from heterogeneity analysis and to compare the structural dynamics observed from CryoEM data with results from other experimental and simulation techniques.

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Metadata

Authors
Chen, M.
Affiliations
SLAC National Accelerator Laboratory (US)
Corresponding author
Chen, Muyuan
ORCID
Chen, Muyuan
Venue
Communications Biology
Publisher
Springer Science and Business Media LLC
Published
2025-05-25
Volume
8
Issue
1
Pages
798-798
ISSN
2399-3642 (ISSN-L)
DOI
10.1038/s42003-025-08202-9
PMC
PMC12104439
OpenAlex
W4410717190
Cited by
11
References
2
Citations by year
2026: 6 · 2025: 5
FWCI
3.96
Type
journal article
Language
en
Open access
Licence
Locations
  • Communications Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R01GM150905)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
conformational heterogeneity, Gaussian mixture model, deep neural network, macromolecular dynamics, heterogeneity analysis

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