SPARX, a new environment for Cryo-EM image processing.

By Michael H. Hohn, Grant Tang, Grant Goodyear, Philip Baldwin, Zhong Huang, Pawel A. Penczek, Chao Yang, R. Glaeser, Paul D. Adams, Steven J. Ludtke. Journal of Structural Biology, 2007

398 citations recorded by the source corpus.

Subfields: Materials Chemistry, Structural Biology, Surfaces, Coatings and Films

View Paper: https://www.semanticscholar.org/paper/de42030e7781613abd650cb9234c7e4832a727fa

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Citations in the corpus

Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association (2016, methodology): “M. Hohn, G. Tang, G. Goodyear, P. R. Baldwin, Z. Huang, P. A. Penczek, C. Yang, R. M. Glaeser, P. D. Adams, S. J. Ludtke, SPARX, a new environment for Cryo-EM image processing.”
Transcriptome engineering with RNA-targeting Type VI-D CRISPR effectors (2018, neutral): “ID=KRE6P5E8Z COOT Emsley et al., 2010 https://www2.mrc-lmb.cam.ac.uk/personal/ pemsley/coot/ PHENIX Adams et al., 2010 http://www.phenix-online.org/ PyMOL Open-Source PyMOL 1.8.x http://www.pymol.org/ UCSF Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/ Leginon Suloway et al., 2005 ”
A Primer to Single-Particle Cryo-Electron Microscopy (2015, neutral): “After direct detectors and movies were adopted, near-atomic resolution was achieved with several software packages, including SPIDER (Frank et al., 1981), EMAN2 (Tang et al., 2007), FREALIGN (Grigorieff, 2007), RELION 442 Cell 161, April 23, 2015 ª2015 Elsevier Inc. (Scheres, 2012), and SPARX (Hohn ”
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 (2016, background): “, 2007), sparx (Hohn et al., 2007), frealign (Grigorieff, 2007), xmipp (Scheres et al.”
A structural model of the active ribosome-bound membrane protein insertase YidC (2014, background): “, 1987), classification, clustering and backprojection of stable classes into 3D (van Heel and Keegstra, 1981; Hohn et al., 2007; Elmlund and Elmlund, 2012).”
Reconstructing continuous distributions of 3D protein structure from cryo-EM images (2019, methodology): “uction with stochastic gradient descent (Punjani et al. (2017)). Once an initial model is generated, there are many tools for iterative reﬁnement of the model (Scheres (2012b); Punjani et al. (2017); Hohn et al. (2007); Lyumkis, Dmitry et al. (2013); Tang et al. (2007)). For example, Scheres (2012a)”
New tools for automated cryo-EM single-particle analysis in RELION-4.0 (2021, methodology): “Developments in SPARX [7], BSOFT [8], FREALIGN [9] and XMIPP [10] also”
Complete subunit architecture of the proteasome regulatory particle (2012, positive): “Three-dimensional maps were calculated using libraries from the EMAN2 and SPARX software packages 45,46 .”
Appion: an integrated, database-driven pipeline to facilitate EM image processing (2009, neutral): “Attempts to unify some of these packages have been made, combining libraries and infrastructure to streamline the transfer of data between routines under a single processing environment but unifying packages are currently not in wide-spread use (Hohn et al., 2007).”
Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation (2014, methodology): “Particles were preprocessed in Appion (45) before projection matching refinement with libraries from EMAN2 and SPARX (59, 60) using RCT reconstructions (34) as initial models.”