Appion citations¶

Appion includes software from the following packages:

$title, $year, $authorlist, $journal, $volume=false, $issue=false, $pmid=false, $pmcid=false, $doi=false, $logo=false

EMAN¶

"EMAN: semiautomated software for high-resolution single-particle reconstructions." (1999) Ludtke SJ, Baldwin PR, Chiu W. J Struct Biol. v128(1). PMID: 10600563

SPIDER¶

"SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields." (1996) Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A. J Struct Biol. v116(1). PMID: 8742743

IMAGIC¶

"A New Generation of the IMAGIC Image Processing System." (1996) van Heel M., Harauz G., Orlova E. V., Schmidt R. & Schatz M. J Struct Biol. v116(1). PMID: 8742718

Appion¶

"Appion: an integrated, database-driven pipeline to facilitate EM image processing." (2009) Lander GC, Stagg SM, Voss NR, et al.. J Struct Biol. v166(1). PMID: 19263523 Free text: PMC2775544 DOI: 10.1016/j.jsb.2009.01.002

Frealign¶

FREALIGN: high-resolution refinement of single particle structures.", 2007, "Grigorieff, N.", "J Struct Biol.", 157, 1, 16828314, false, "10.1016/j.jsb.2006.05.004", "img/grigorieff_lab.png");

Initial Model¶

A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.", 2010, "Voss NR, Lyumkis D, Cheng A, <i>et al.</i>", "J Struct Biol.", 169, 3, 20018246, false, false, "img/topbarbackgrnd.jpg");

Dog Picking¶

"DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy." (2009) Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B. J Struct Biol. v166(2). PMID: 19374019 Free text: PMC2768396

ACE¶

"ACE: automated CTF estimation." (2005) Mallick SP, Carragher B, Potter CS, Kriegman DJ. Ultramicroscopy. v104(1). PMID: 15935913

CTFfind¶

"Accurate determination of local defocus and specimen tilt in electron microscopy." (2003) Mindell, JA, Grigorieff N. J Struct Biol. v142(3). PMID: 12781660

XMIPP¶

"Maximum-likelihood multi-reference refinement for electron microscopy images." (2005) Scheres SH, Valle M, Nuñez R, Sorzano CO, Marabini R, Herman GT, Carazo JM. J Mol Biol. v348(1). PMID: 15808859
"Fast maximum-likelihood refinement of electron microscopy images." (2005) Scheres SH, Valle M, Carazo JM. Bioinformatics. v21(Suppl 2). PMID: 16204112

CAN Reference-free Alignment¶

"Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking." (2003) Ogura T, Iwasaki K, Sato C. J Struct Biol. v143(3). PMID: 14572474