Cited by 886Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and FunctionProtein Structure and Dynamics

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

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Barad, Benjamin A, Echols, Nathaniel, Wang, Ray Yu-Ruei, Cheng, Yifan, DiMaio, Frank, Adams, Paul D, Fraser, James S·2015·Nature Methods

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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
Venue
Nature Methods
Published
2015-08-17
Volume
12
Issue
10
Pages
943-946
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
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
Licence
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

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