Structural Study of Heterogeneous Biological Samples by Cryoelectron Microscopy and Image Processing

Table 1

Packages used to work with heterogeneous datasets.

Package name	Package reference	Examples	Statistical; Method used	References
IMAGIC	Van Heel et al., 1996 [32],; https://www.imagescience.de/imagic_em.html	Hsp26; GroEL-Rhodanese; 70Sribosome and the U4/U6.U5 tri-snRNP	MSA	White et al., 2004 [33]; Elad et al., 2008 [5]; Sander et al., 2010 [30]
SPIDER	Frank et al., 1996 [34],; http://www.wadsworth.org/spider_doc/spider	70S ribosome; 70S ribosome, tRNAs & elongation factor; G (EF-G) complexes	MSA; BS	Liao and Frank, 2010 [35] (for bootstrapping volume calculation); Penczek et al., 2006 [36]
RELION	Scheres, 2012 [37]; Scheres, 2015 [38],; https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page	70S ribosome complex; Ltn1 E3 ligase (four model refinements); Subtomogram averaging	ML (regularized likelihood optimization),; BS	Anden et al., 2015 [39]; Lyumkis et al., 2013 [13]; Bharat and Scheres, 2016 [40]
EMAN2	http://blake.bcm.edu/emanwiki/EMAN2	Beta-galactosidase; GroEL, Ca2+ release channel	MSA, BS, CM	Tang et al., 2007 [41],; https://www.youtube.com/c/SteveLudtke
SPARX	Hohn et al., 2007 [42],; http://blake.bcm.edu/emanwiki/EMAN2	70S ribosome; 70S ribosome; Ltn1 E3 ligase (single model refinement)	BS,CM	Liao and Frank, 2010 [35] (for eigendecomposition); Penczek et al., 2011 [28]; Lyumkis et al., 2013 [13]
XMIPP	Sorzano et al., 2004 [43]; De la Rosa-Trevín et al., 2013 [44],; http://xmipp.cnb.csic.es/	70S ribosome & Simian Virus 40 large T-antigen; groEL/groES complexes; & p53; B. Subtilis G40P helicase & SV40 large T-antigen	ML; NN	Scheres et al., 2007 [45, 46]; Scheres et al., 2009 [47]; Pascual-Montano et al., 2001 [48]
ASPIRE	(http://spr.math.princeton.edu/)	70S ribosome	CM	Katsevich et al., 2015 [49]
FREALIGN	Grigorieff 2007 [50]; http://grigoriefflab.janelia.org/frealign	70S ribosome	ML	Lyumkis et al., 2013 [51]
Appion	http://www.appion.org	integration of different software packages		Lander et al., 2009 [52]
Scipion	http://scipion.cnb.csic.es	shell that combined different packages		de la Rosa-Trevín et al., 2016 [53]

MSA: multivariate statistical analysis; ML: maximum likelihood; BS: bootstrapping; CM: covariance maps; NN: neural networks. For more software packages see http://www.emdatabank.org/emsoftware.html.