Appion citations » History » Revision 17
Revision 16 (Amber Herold, 01/12/2011 12:40 PM) → Revision 17/29 (Amber Herold, 01/12/2011 12:40 PM)
h1. Appion Citations Appion includes software from the following packages: h3. ACE * "ACE: automated CTF estimation." (2005) Mallick SP, Carragher B, Potter CS, Kriegman DJ. Ultramicroscopy. v104(1). PMID: 15935913 h3. 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 * "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 h3. 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 h3. Chimera * 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. * "More on Chimera Citations":http://www.cgl.ucsf.edu/chimera/docs/credits.html h3. Clustering by Affinity Propogation * "Clustering by Passing Messages Between Data Points." (2007) Brendan J. Frey and Delbert Dueck. Science. v315(5814). PMID: 17218491 h3. CTFFind * "Accurate determination of local defocus and specimen tilt in electron microscopy." (2003) Mindell, JA, Grigorieff N. J Struct Biol. v142(3). PMID: 12781660 h3. CTFTilt * 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 "PMID:12781660"::http://www.ncbi.nlm.nih.gov/pubmed/12781660 h3. DogPicker * "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 h3. EMAN * "EMAN: semiautomated software for high-resolution single-particle reconstructions." (1999) Ludtke SJ, Baldwin PR, Chiu W. J Struct Biol. v128(1). PMID: 10600563 h3. EM-BFACTOR h3. FindEM h3. Frealign * "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 h3. 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 h3. IMOD h3. ProTomo h3. RMeasure h3. 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 h3. TiltPicker h3. 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 * "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 * "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