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Appion citations » History » Version 19

Amber Herold, 01/12/2011 12:48 PM

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h1. Appion Citations
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Appion includes software from the following packages:
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h3. ACE
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* "ACE: automated CTF estimation." (2005) Mallick SP, Carragher B, Potter CS, Kriegman DJ. Ultramicroscopy. v104(1).  PMID: 15935913 
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h3. Appion
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* "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 
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* "A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy." (2010) Voss NR, Lyumkis D, Cheng A, et al.. J Struct Biol. v169(3).  PMID: 20018246
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h3. CAN Reference-free Alignment
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* "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  
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h3. Chimera
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* Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR001081). "UCSF Chimera--a visualization system for exploratory research and analysis":http://www.ncbi.nlm.nih.gov/pubmed/15264254. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.
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* "More on Chimera Citations":http://www.cgl.ucsf.edu/chimera/docs/credits.html
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h3. Clustering by Affinity Propogation
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* "Clustering by Passing Messages Between Data Points." (2007) Brendan J. Frey and Delbert Dueck. Science. v315(5814).  PMID: 17218491  
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h3. CTFFind
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* "Accurate determination of local defocus and specimen tilt in electron microscopy." (2003) Mindell, JA, Grigorieff N. J Struct Biol. v142(3).  PMID: 12781660  
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h3. CTFTilt
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* Mindell JA, GrigorieV N (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol 142:334–347. "PMID:12781660":http://www.ncbi.nlm.nih.gov/pubmed/12781660
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h3. DogPicker
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* "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  
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h3. EMAN
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* "EMAN: semiautomated software for high-resolution single-particle reconstructions." (1999) Ludtke SJ, Baldwin PR, Chiu W. J Struct Biol. v128(1).  PMID: 10600563  
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h3. EM-BFACTOR
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* "Optimal Determination of Particle Orientation":http://dx.doi.org/10.1016/j.jmb.2003.07.013, Absolute Hand and Contrast Loss in Single-particle Electron Cryomicroscopy P.B. Rosenthal and R. Henderson Journal of Molecular Biology 333:721-745, 2003.
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* "Sharpening high resolution information in single particle electron cryomicroscopy":http://dx.doi.org/10.1016/j.jsb.2008.05.010 J.J. Fernandez, D. Luque, J.R. Caston, J.L. Carrascosa Journal of Structural Biology 164:170-175, 2008. PMID:18614378
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h3. FindEM
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h3. Frealign
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* "FREALIGN: high-resolution refinement of single particle structures." (2007) Grigorieff, N. J Struct Biol. v157(1).  PMID: 16828314  DOI: 10.1016/j.jsb.2006.05.004  
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h3. IMAGIC
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* "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  
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h3. IMOD
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h3. ProTomo
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h3. RMeasure
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h3. SPIDER
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* "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 
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h3. TiltPicker
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h3. XMIPP
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* "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  
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* "Fast maximum-likelihood refinement of electron microscopy images." (2005) Scheres SH, Valle M, Carazo JM. Bioinformatics. v21(Suppl 2).  PMID: 16204112
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* "A Novel Neural Network Technique for Analysis and Classification of EM Single-Particle Images." (2001) A. Pascual-Montano, L. E. Donate, M. Valle, M. Bárcena, R. D. Pascual-Marqui, J. M. Carazo. J Struct Biol. v133(2/3).  PMID: 11472094  
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* "XMIPP: a new generation of an open-source image processing package for electron microscopy." (2004) Sorzano CO, Marabini R, Velázquez-Muriel J, Bilbao-Castro JR, Scheres SH, Carazo JM, Pascual-Montano A. J Struct Biol. v148(2).  PMID: 15477099  DOI: 10.1016/j.jsb.2004.06.006