The DOI matches its Crossref record; 73 of the 73 references it cites were found in a registry or an index.
emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging
Open accessAbstract
Macromolecular complexes are intrinsically flexible and often challenging to purify for structure determination by single-particle cryo-electron microscopy (cryo-EM). Such complexes can be studied by cryo-electron tomography (cryo-ET) combined with subtomogram alignment and classification, which in exceptional cases achieves subnanometer resolution, yielding insight into structure–function relationships. However, it remains challenging to apply this approach to specimens that exhibit conformational or compositional heterogeneity or are present in low abundance. To address this, we developed emClarity (https://github.com/bHimes/emClarity/wiki), a GPU-accelerated image-processing package featuring an iterative tomographic tilt-series refinement algorithm that uses subtomograms as fiducial markers and a 3D-sampling-function-compensated, multi-scale principal component analysis classification method. We demonstrate that our approach offers substantial improvement in the resolution of maps and in the separation of different functional states of macromolecular complexes compared with current state-of-the-art software. A software tool, emClarity, implements several improvements in cryo-electron tomography image-processing algorithms to achieve sub-nanometer resolution for diverse macromolecular structures.
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A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0
Zivanov, J., Otón, J., Ke, Z., von Kügelgen, A., Pyle, E., Qu, K., Morado, D., Castaño-Díez, D., Zanetti, G., Bharat, T. A., et al. (2022) · eLife · doi:10.7554/elife.83724 · Cited by 339
In-cell architecture of an actively transcribing-translating expressome
O’Reilly, F. J., Xue, L., Graziadei, A., Sinn, L., Lenz, S., Tegunov, D., Blötz, C., Singh, N., Hagen, W. J. H., Cramer, P., et al. (2020) · Science · doi:10.1126/science.abb3758 · Cited by 284
A complete data processing workflow for cryo-ET and subtomogram averaging
Chen, M., Bell, J. M., Shi, X., Sun, S. Y., Wang, Z., & Ludtke, S. J. (2019) · Nature Methods · doi:10.1038/s41592-019-0591-8 · Cited by 253
Barad, B. A., Medina, M., Fuentes, D., Wiseman, R. L., & Grotjahn, D. A. (2023) · Journal of Cell Biology · doi:10.1083/jcb.202204093 · Cited by 81
A cryo-ET survey of microtubules and intracellular compartments in mammalian axons
Foster, H. E., Ventura Santos, C., & Carter, A. P. (2022) · Journal of Cell Biology · doi:10.1083/jcb.202103154 · Cited by 69
Metadata
- Authors
- Himes, B. A., & Zhang, P.
- Venue
- Nature Methods
- Published
- 2018-10-22
- Volume
- 15
- Issue
- 11
- Pages
- 955-961
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2897254286
- Cited by
- 283
- References
- 73
- FWCI
- 10.60
- Type
- journal article
- Language
- en
- Open access
- green
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