EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
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Abstract
Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report EMRinger, a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.
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- Authors
- Barad, B. A., Echols, N., Wang, R. Y.-R., Cheng, Y., DiMaio, F., Adams, P. D., & Fraser, J. S.
- Affiliations
- University of California, San Francisco (US)
- Lawrence Berkeley National Laboratory (US)
- University of Washington (US)
- Corresponding author
- Fraser, James S
- ORCID
- Venue
- Nature Methods
- Published
- 2015-08-17
- Volume
- 12
- Issue
- 10
- Pages
- 943-946
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC4589481
- OpenAlex
- W1838872057
- Cited by
- 886
- References
- 58
- Citations by year
- 2026: 57 · 2025: 84 · 2024: 83 · 2023: 81 · 2022: 119 · 2021: 99 · 2020: 136 · 2019: 89 · 2018: 77 · 2017: 39 · 2016: 20 · 2015: 1
- FWCI
- 23.16
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (1231306)
- National Institutes of Health (DP5OD009180, GM082250, GM063210)
- National Institute of General Medical Sciences (P01GM063210, R01GM082893, T32GM008284, P50GM082250, GM110580, GM098672, GM063210, GM082250, GM082893, R21GM110580, R01GM098672)
- National Institute of Biomedical Imaging and Bioengineering (T32EB009383)
- 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
- model validation, radiation damage, negatively charged amino acids
- MeSH terms
- Image Processing, Computer-Assisted, Models, Molecular, Protein Conformation, Proteins, Software, Reproducibility of Results, Crystallography, X-Ray, Cryoelectron Microscopy, Databases, Protein, TRPV Cation Channels
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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