Bibliography

[BMR+19]

Tristan Bepler, Andrew Morin, Micah Rapp, Julia Brasch, Lawrence Shapiro, Alex J. Noble, and Bonnie Berger. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nature Methods, 2019. doi:10.1038/s41592-019-0575-8.

[BRL+15]

Tanmay A. M. Bharat, Christopher J. Russo, Jan Löwe, Lori A. Passmore, and Sjors H. W. Scheres. Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging. Structure (London, England: 1993), 23(9):1743–1753, September 2015. doi:10.1016/j.str.2015.06.026.

[CMF+13]

Shaoxia Chen, Greg McMullan, Abdul R. Faruqi, Garib N. Murshudov, Judith M. Short, Sjors H. W. Scheres, and Richard Henderson. High-resolution noise substitution to measure overfitting and validate resolution in 3d structure determination by single particle electron cryomicroscopy. Ultramicroscopy, 135:24–35, December 2013. doi:10.1016/j.ultramic.2013.06.004.

[ELSC10]

Paul Emsley, Bernhard Lohkamp, William G. Scott, and Kevin Cowtan. Features and development of coot. Acta Crystallographica Section D - Biological Crystallography, 66:486–501, 2010. doi:10.1107/S0907444910007493.

[FLS17]

Rafael Fernandez-Leiro and Sjors H. W. Scheres. A pipeline approach to single-particle processing in RELION. Acta Crystallographica. Section D, Structural Biology, 73(Pt 6):496–502, June 2017. doi:10.1107/S2059798316019276.

[HS17]

Shaoda He and Sjors H. W. Scheres. Helical reconstruction in RELION. Journal of Structural Biology, 2017. doi:10.1016/j.jsb.2017.02.003.

[JBH05]

David M Belnap J Bernard Heymann, Mónica Chagoyen. Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. Journal of Structural Biology, 151(2):196–207, 2005.

[JKZ+23]

Kiarash Jamali, Lukas Kall, Rui Zhang, Alan Brown, Dari Kimanius, and Sjors Scheres. Automated model building and protein identification in cryo-em maps. bioRxiv, 2023. doi:10.1101/2023.05.16.541002.

[KFSL16]

Dari Kimanius, Björn O Forsberg, Sjors HW Scheres, and Erik Lindahl. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. eLife, November 2016. doi:10.7554/eLife.18722.

[KST14]

Alp Kucukelbir, Fred J Sigworth, and Hemant D Tagare. Quantifying the local resolution of cryo-EM density maps. Nature methods, 11(1):63–65, January 2014. doi:10.1038/nmeth.2727.

[MG03]

Joseph A Mindell and Nikolaus Grigorieff. Accurate determination of local defocus and specimen tilt in electron microscopy. Journal of Structural Biology, 142(3):334–347, 2003.

[PRFB17]

Ali Punjani, John L. Rubinstein, David J. Fleet, and Marcus A. Brubaker. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nature Methods, 14(3):290–296, March 2017. doi:10.1038/nmeth.4169.

[RG15]

Alexis Rohou and Nikolaus Grigorieff. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. Journal of Structural Biology, 192(2):216–221, November 2015. doi:10.1016/j.jsb.2015.08.008.

[RH03]

Peter B Rosenthal and Richard Henderson. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology, 333(4):721–745, October 2003.

[Sch10]

Sjors H W Scheres. Classification of Structural Heterogeneity by Maximum-Likelihood Methods. In Cryo-EM, Part B: 3-D Reconstruction, volume 482 of Methods in Enzymology, pages 295–320. Academic Press, 2010.

[Sch12a]

Sjors H W Scheres. A Bayesian view on cryo-EM structure determination. Journal of Molecular Biology, 415(2):406–418, January 2012. doi:10.1016/j.jmb.2011.11.010.

[Sch12b]

Sjors H W Scheres. RELION: Implementation of a Bayesian approach to cryo-EM structure determination. Journal of Structural Biology, 180(3):519–530, December 2012. doi:10.1016/j.jsb.2012.09.006.

[SC12]

Sjors H W Scheres and Shaoxia Chen. Prevention of overfitting in cryo-EM structure determination. Nature methods, 9(9):853–854, September 2012. doi:10.1038/nmeth.2115.

[SNRS+08]

Sjors H W Scheres, R. Nunez-Ramirez, C. O. S Sorzano, J. M Carazo, and R. Marabini. Image processing for electron microscopy single-particle analysis using XMIPP. Nature Protocols, 3(6):977–90, 2008.

[SKB+23]

Johannes Schwab, Dari Kimanius, Alister Burt, Tom Dendooven, and Sjors Scheres. Dynamight: estimating molecular motions with improved reconstruction from cryo-em images. bioRxiv, 2023. doi:10.1101/2023.10.18.562877.

[Smi99]

J M Smith. Ximdisp–A visualization tool to aid structure determination from electron microscope images. Journal of structural biology, 125(2-3):223–228, May 1999. doi:10.1006/jsbi.1998.4073.

[TPB+07]

Guang Tang, Liwei Peng, Philip R Baldwin, Deepinder S Mann, Wen Jiang, Ian Rees, and Steven J Ludtke. EMAN2: an extensible image processing suite for electron microscopy. Journal of Structural Biology, 157(1):38–46, January 2007. doi:10.1016/j.jsb.2006.05.009.

[YPBM21]

Keitaro Yamashita, Colin M. Palmer, Tom Burnley, and Garib N. Murshudov. Cryo-EM single-particle structure refinement and map calculation using \it Servalcat. Acta Crystallographica Section D, 77(10):1282–1291, Oct 2021. doi:10.1107/S2059798321009475.

[Zha16]

Kai Zhang. Gctf: Real-time CTF determination and correction. Journal of Structural Biology, 193(1):1–12, January 2016. doi:10.1016/j.jsb.2015.11.003.

[ZPA+17]

Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A. Verba, Yifan Cheng, and David A. Agard. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nature Methods, 14(4):331–332, April 2017. doi:10.1038/nmeth.4193.

[ZNS20]

Jasenko Zivanov, Takanori Nakane, and Sjors Scheres. Estimation of high-order aberrations and anisotropic magnification from cryo-em datasets in relion-3.1. IUCrJ, 2020. doi:10.1107/S2052252520000081.