The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
New tools for automated cryo-EM single-particle analysis in RELION-4.0
Open accessAbstract
We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in the fourth major release of the RELION software. In particular, we introduce VDAM, a variable-metric gradient descent algorithm with adaptive moments estimation, for image refinement; a convolutional neural network for unsupervised selection of 2D classes; and a flexible framework for the design and execution of multiple jobs in pre-defined workflows. In addition, we present a stand-alone utility called MDCatch that links the execution of jobs within this framework with metadata gathering during microscope data acquisition. The new tools are aimed at providing fast and robust procedures for unsupervised cryo-EM structure determination, with potential applications for on-the-fly processing and the development of flexible, high-throughput structure determination pipelines. We illustrate their potential on 12 publicly available cryo-EM data sets.
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Cites
Adam: A Method for Stochastic Optimization
Kingma, D. P., & Ba, J. (2014) · arXiv · doi:10.48550/arxiv.1412.6980 · Cited by 98,946
RELION: Implementation of a Bayesian approach to cryo-EM structure determination
Scheres, S. H. W. (2012) · Journal of Structural Biology · doi:10.1016/j.jsb.2012.09.006 · Cited by 5,446
Self-citationADADELTA: An Adaptive Learning Rate Method
Zeiler, M. D. (2012) · arXiv · doi:10.48550/arxiv.1212.5701 · Cited by 5,322
Kühlbrandt, W. (2014) · Science · doi:10.1126/science.1251652 · Cited by 1,325
Cited by
Automated model building and protein identification in cryo-EM maps
Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2023) · doi:10.1101/2023.05.16.541002 · Cited by 686
Self-citationAutomated model building and protein identification in cryo-EM maps
Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2024) · Nature · doi:10.1038/s41586-024-07215-4 · Cited by 686
Self-citationStructural conservation of antibiotic interaction with ribosomes
Paternoga, H., Crowe-McAuliffe, C., Bock, L. V., Koller, T. O., Morici, M., Beckert, B., Myasnikov, A. G., Grubmüller, H., Nováček, J., & Wilson, D. N. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01047-y · Cited by 94
Kubo, S., Black, C. S., Joachimiak, E., Yang, S. K., Legal, T., Peri, K., Khalifa, A. A. Z., Ghanaeian, A., McCafferty, C. L., Valente-Paterno, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37868-0 · Cited by 93
Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome
Healy, M. D., McNally, K. E., Butkovič, R., Chilton, M., Kato, K., Sacharz, J., McConville, C., Moody, E. R. R., Shaw, S., Planelles-Herrero, V. J., et al. (2023) · Cell · doi:10.1016/j.cell.2023.04.003 · Cited by 91
Metadata
- Authors
- Kimanius, D., Dong, L., Sharov, G., Nakane, T., & Scheres, S. H. W.
- Venue
- Biochemical Journal
- Publisher
- Portland Press Ltd.
- Published
- 2021-12-16
- Volume
- 478
- Issue
- 24
- Pages
- 4169-4185
- ISSN
- 0264-6021 (ISSN-L)
- 1470-8728
- OpenAlex
- W3213779066
- Cited by
- 1,086
- References
- 4
- FWCI
- 58.50
- Type
- journal article
- Language
- en
- Open access
- hybrid
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