Student or educator? Sign up with your school email and get 6 months of Pro free.
Cited by 1,683

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction

Open access
Punjani, Ali, Zhang, Haowei, Fleet, David J.·2020·Nature Methods

Published version of a preprint

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41592-020-00990-8

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 6 references

Research works printed but not linked: 37

  1. Cheng, Y. Single-particle Cryo-EM at crystallographic resolution. Cell 161, 450–457 (2015). · DOI · Paper page
  2. Cheng, Y. Membrane protein structural biology in the era of single particle cryo-EM. Curr. Opin. Struct. Biol. 52, 58–63 (2018). · DOI
  3. Renaud, J.-P. et al. Cryo-EM in drug discovery: achievements, limitations and prospects. Nat. Rev. Drug Discov. 17, 471–492 (2018). · DOI · Paper page
  4. Scapin, G., Potter, C. S. & Carragher, B. Cryo-EM for small molecules discovery, design, understanding, and application. Cell Chem. Biol. 25, 1318–1325 (2018). · DOI
  5. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. CryoSPARC: Algorithms for rapid unsupervised cryo-em structure determination. Nat. Methods 14, 290–296 (2017). · DOI · Paper page
  6. Grigorieff, N. FREEALIGN: High resolution refinement of single particle structures. J. Struct. Biol. 157, 117–125 (2007). · DOI · Paper page
  7. Scheres, S. H. W. & Bayesian, A. view on cryo-em structure determination. J. Mol. Biol. 415, 406–418 (2012). · DOI · Paper page
  8. Bell, J. M., Chen, M., Baldwin, P. R. & Ludtke, S. J. High resolution single particle refinement in EMAN2.1. Methods 100, 25–34 (2016). · DOI
  9. Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user-friendly software for single-particle image processing. eLife 7, e35383 (2018). · DOI · Paper page
  10. Zivanov, J. et al. New tools for automated high-resolution cryo-em structure determination in RELION-3. eLife 7, e42166 (2018). · DOI · Paper page
  11. Chen, S. et al. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135, 24–35 (2013). · DOI · Paper page
  12. Harauz, G. & van Heel, M. Exact filters for general geometry three dimensional reconstruction. Optik 73, 146–156 (1986).
  13. Scheres, S. H. W. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. methods 9, 853–854 (2012). · DOI · Paper page
  14. Paulsen, C. E., Armache, J. P., Gao, Y., Cheng, Y. & Julius, D. Structure of the TRPA1 ion channel suggests regulatory mechanisms. Nature 520, 511–517 (2015). · DOI · Paper page
  15. Golub, G. M., Heath, M. & Wahba, G. Generalized cross-validation as as a method for choosing a good ridge parameter. Technometrics 21, 215–223 (1979). · DOI · Paper page
  16. Wahba, G. A comparison of GCV and GML for choosing the smoothing parameter in the generalized spline smoothing problem. Ann. Stat. 13, 1378–1402 (1985). · DOI
  17. Lehtinen, J. et al. Noise2Noise: learning image restoration without clean data. Proc. Mach. Learn. Res. 7, 4620–4631 (2018).
  18. Cardone, G., Heymann, J. B. & Steven, A. C. One number does not fit all: mapping local variations in resolution in cryo-em reconstructions. J. Struct. Biol. 184, 226–236 (2013). · DOI · Paper page
  19. Chen, Y. et al. Structure of the stra6 receptor for retinol uptake. Science 353, aad8266 (2016). · DOI · Paper page
  20. Kim, J. et al. Structure and drug resistance of the Plasmodium falciparum transporter PfCRT. Nature https://doi.org/10.1038/s41586-019-1795-x (2019). · DOI
  21. Xu, H. et al. Structural basis of Nav1.7 inhibition by a gating-modifier spider toxin. Cell https://doi.org/10.1016/j.cell.2018.12.018 (2019). · DOI
  22. Stagg, S., Noble, A., Spilman, M. & Chapman, M. Reslog plots as an empirical metric of the quality of cryo-EM reconstructions. J. Struct. Biol. 185, 418–426 (2014). · DOI
  23. Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014). · DOI · Paper page
  24. Vilas, J. L. et al. Monores: automatic and accurate estimation of local resolution for electron microscopy maps. Structure 26, 337–344 (2018). · DOI
  25. Felsberg, M. & Sommer, G. The monogenic signal. IEEE Trans. Signal Process. 49, 3136–3144 (2001). · DOI · Paper page
  26. Ramlaul, K., Palmer, C. M. & Aylett, C. H. S. A local agreement filtering algorithm for transmission EM reconstructions. J. Struct. Biol. 205, 30–40 (2019). · DOI
  27. Ramlaul, K., Palmer, C. M., Nakane, T. & Aylett, C. H. S. Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER. J. Struct. Biol. 211, 107545 (2020). · DOI
  28. Vonesch, C., Wang, L., Shkolnisky, Y. and Singer, A. Fast wavelet-based single particle reconstruction in cryo-EM. Proc. IEEE Int. Symp. Biomed. Imaging https://doi.org/10.1109/ISBI.2011.5872791 (2011). · DOI
  29. Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. A Bayesian adaptive basis algorithm for single particle reconstruction. J. Struct. Biol. 179, 56–67 (2012). · DOI
  30. Hofmann, S. et al. Conformation space of a heterodimeric ABC exporter under turnover conditions. Nature 571, 580–583 (2019). · DOI
  31. Rogala, K. B. et al. Structural basis for the docking of mTORC1 on the lysosomal surface. Science 366, 468–475 (2019). · DOI · Paper page
  32. Gilman, M. S. A. et al. Structure of the respiratory syncytial virus polymerase complex. Cell 179, 193–204 (2019). · DOI
  33. Nguyen, A. H. et al. Structure of an endosomal signaling GPCR-G protein-β-arrestin megacomplex. Nat. Struct. Mol. Biol. 26, 1123–1131 (2019). · DOI
  34. Bepler, T., Noble, A. & Berger, B. Topaz-Denoise: general deep denoising models for cryoEM. Nat. Commun. 11, 5208 (2020). · DOI · Paper page
  35. Tegunov, D. & Cramer, P. Real-time cryo-electron microscopy data preprocessing with warp. Nat. Methods 16, 1146–1152 (2019). · DOI · Paper page
  36. Buchholz, T.-O., Jordan, M., Pigino, G. & Jug, F. cryoCARE: content-aware image restoration for cryo-transmission electron microscopy data. Preprint at arXiv https://arxiv.org/abs/1810.05420 (2018). · arXiv
  37. Potamianos, A. & Maragos, P. A comparison of the energy operator and the Hilbert transform approach to signal and speech demodulation. Signal Process. 37, 95–120 (1994). · DOI

Cited by

Items 101–150 of 150

Metadata

Authors
Punjani, A., Zhang, H., & Fleet, D. J.
Venue
Nature Methods
Published
2020-11-30
Volume
17
Issue
12
Pages
1214-1221
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
OpenAlex
W3108495343
Cited by
1,683
References
6
FWCI
61.85
Type
journal article
Language
en
Open access
green
Licence
Funders
Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (USRA, RGPIN 2015-05630)

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 ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.