Appion citations » History » Revision 26
Revision 25 (Amber Herold, 01/12/2011 01:43 PM) → Revision 26/29 (Amber Herold, 01/12/2011 01:46 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
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. Ed's Iteration Alignment
* "Conformational flexibility of metazoan fatty acid synthase enables catalysis." (2009) Brignole EJ, Smith S, Asturias FJ., Nat Struct Mol Biol., v.16(2). PMID: 19151726, PMCID: 2653270
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
* "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.
* "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
h3. FindEM
* "FindEM--a fast, efficient program for automatic selection of particles from electron micrographs." (2004) Roseman AM., J Struct Biol., Volume 145, Issues 1-2. PMID: 15065677
* Roseman, 2003. A.M. Roseman, Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy 94 (2003), pp. 225–236.
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
* Kremer J.R., D.N. Mastronarde and J.R. McIntosh (1996) Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116:71-76. PMID: 8742726
h3. ProTomo
* "The Use of Electron Tomography for Structural Analysis of Disordered Protein Arrays" K. A. Taylor, J. Tang, Y. Cheng and H. Winkler, J. Struct. Biol. 120, 372-386, 1997.
* "Focus gradient correction applied to tilt series image data used in electron tomography" H. Winkler, K. A. Taylor, J. Struct. Biol. 143, 24-32, 2003.
* "Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography" H. Winkler and K. A. Taylor, Ultramicroscopy 106, 240-254, 2006.
* "3D reconstruction and processing of volumetric data in cryo-electron tomography" H. Winkler, J. Struct. Biol. 157, 126-137, 2007.
h3. RMeasure
* Sousa, D, Grigorieff N. 2007. Ab initio resolution measurement for single particle structures. J Struct Biol. 157:201-10.
h3. SIGNATURE
* "SIGNATURE: a single-particle selection system for molecular electron microscopy." (2007) Chen JZ, Grigorieff N., J Struct Biol. v.157(1) PMID: 16870473
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
* Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B. (2009) "DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy":http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768396/. J Struct Biol. v166(2): pp. 205-13.
h3. Tomogram Maker
* "Dual-axis tomography: an approach with alignment methods that preserve resolution." (1997) D.N. Mastronarde, J. Struct. Biol. v.120(3) PMID: 9441937 doi:10.1006/jsbi.1997.3919
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