SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs

By T. Shaikh, Haixiao Gao, W. T. Baxter, F. Asturias, N. Boisset, ArDean Leith, Joachim Frank. Nature Protocols, 2008

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Structural Dynamics of the YidC:Ribosome Complex during Membrane Protein Biogenesis (2016, methodology): “Initial alignment of 33 binned data was performed using the SPIDER software package (Shaikh et al., 2008), providing an empty 70S ribosome as a reference, and resulted in a ribosome with strong densities for tRNA and a nanodisc.”
Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning (2016, unknown): “Using the simulated data, we compared the results from our approach with those obtained using RELION [19], EMAN2 [47] and SPIDER [20].”
RELION: Implementation of a Bayesian approach to cryo-EM structure determination (2012, methodology): “02) (Shaikh et al., 2008): one using a Kaiser–Bessel interpolation kernel (commands PR3Q and BP3F), the other using gridding (Penczek et al.”
Gctf: Real-time CTF determination and correction (2015, methodology): “There are currently several programs available for CTF determination (Ludtke et al., 1999; Mallick et al., 2005; Mindell and Grigorieff, 2003; Penczek et al., 2014; Shaikh et al., 2008; Sorzano et al., 2004; Tang et al., 2007; Vargas et al., 2013; Voortman et al., 2011).”