EMAN: semiautomated software for high-resolution single-particle reconstructions.

By Steven J. Ludtke, Philip Baldwin, Wah Chiu. 1999

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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).”
XMIPP: a new generation of an open-source image processing package for electron microscopy. (2004, methodology): “Several comprehensive software packages for single-particle reconstruction are available to the electron microscopist, e.g., Spider (Frank et al., 1996), Imagic (van Heel et al., 1996), or Eman (Ludtke et al., 1999).”
Negative Staining and Image Classification – Powerful Tools in Modern Electron Microscopy (2004, background): “IMAGIC (24) is commercially available, whereas SPIDER (14) and EMAN (25) are academic packages.”
Bridging the information gap: computational tools for intermediate resolution structure interpretation. (2001, methodology): “Portions from these structures, 1C3W (5-99), 1TIM (1-64), 1IRK (981-1078) and 1BVP trimer (117-261), were extracted (column 1, red) and modeled at 8 AÊ resolution (column 2).”
Blind deconvolution in scientific imaging & computational photography (2011, methodology): “We used the program pdb2mrc from the EMAN software package (Ludtke et al., 1999) for density map simulation.”
FREALIGN: high-resolution refinement of single particle structures. (2007, methodology): “FREALIGN differs from other well-established image processing packages, such as SPIDER (Frank et al., 1996), IMAGIC (van Heel et al., 1996) and EMAN ( Ludtke et al., 1999 ).”
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex (2009, methodology): “, particles comprising aggregates—via 12 cycles of EMAN projection-based matching particle classification (48) interleaved with SPIDER (49) correspondence analysis (procedure as described in (46); SPIDER reference-free classification is performed on each EMAN class and the SPIDER class with highest ”