Cryo‐EM model validation using independent map reconstructions
Open accessAbstract
An increasing number of cryo‐electron microscopy (cryo‐EM) density maps are being generated with suitable resolution to trace the protein backbone and guide sidechain placement. Generating and evaluating atomic models based on such maps would be greatly facilitated by independent validation metrics for assessing the fit of the models to the data. We describe such a metric based on the fit of atomic models with independent test maps from single particle reconstructions not used in model refinement. The metric provides a means to determine the proper balance between the fit to the density and model energy and stereochemistry during refinement, and is likely to be useful in determining values of model building and refinement metaparameters quite generally.
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Overfitting of the model was monitored and controlled with a half-map approach: one half-map was used for density-guided refinement and the other for validation.
“Model overfitting was monitored and contained using the half-map approach as previously described64,65, in which one-half map from RELION Refine3d was used for density-guided refinement, whereas the other half map was used for validation.”
From Structure of Hsp90–Hsp70–Hop–GR reveals the Hsp90 client-loading mechanism (2022) · cites this paper as [64]
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- Authors
- DiMaio, F., Zhang, J., Chiu, W., & Baker, D.
- Affiliations
- University of Washington (US)
- Stanford Medicine (US)
- Baylor College of Medicine (US)
- Corresponding author
- Baker, David
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2013-05-25
- Volume
- 22
- Issue
- 6
- Pages
- 865-868
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- PMC
- PMC3690725
- OpenAlex
- W2131495934
- Cited by
- 72
- References
- 18
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 1 · 2022: 5 · 2021: 7 · 2020: 10 · 2019: 5 · 2018: 3 · 2017: 4 · 2016: 14 · 2015: 13 · 2014: 6 · 2013: 2
- FWCI
- 6.38
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Protein Science (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- NIH (P41GM103832, PN2EY016525, R01GM079429, and R01GM092802)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- cryo-electron microscopy, model validation, single-particle reconstruction, model refinement, stereochemistry, model development, protein structure
- MeSH terms
- Models, Molecular, Chaperonins, Thermococcus, Archaeal Proteins, Cryoelectron Microscopy
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