Appion citations » History » Version 16
Amber Herold, 01/12/2011 12:40 PM
| 1 | 11 | Amber Herold | h1. Appion Citations |
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| 2 | 1 | Amber Herold | |
| 3 | 2 | Amber Herold | Appion includes software from the following packages: |
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| 6 | 10 | Amber Herold | h3. ACE |
| 7 | 2 | Amber Herold | |
| 8 | 10 | Amber Herold | * "ACE: automated CTF estimation." (2005) Mallick SP, Carragher B, Potter CS, Kriegman DJ. Ultramicroscopy. v104(1). PMID: 15935913 |
| 9 | 1 | Amber Herold | |
| 10 | 2 | Amber Herold | h3. Appion |
| 11 | 1 | Amber Herold | |
| 12 | * "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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| 13 | * "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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| 15 | 10 | Amber Herold | h3. CAN Reference-free Alignment |
| 16 | 2 | Amber Herold | |
| 17 | 10 | Amber Herold | * "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 |
| 18 | 2 | Amber Herold | |
| 19 | 12 | Amber Herold | |
| 20 | h3. Chimera |
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| 22 | 14 | Amber Herold | * 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. |
| 23 | 13 | Amber Herold | * "More on Chimera Citations":http://www.cgl.ucsf.edu/chimera/docs/credits.html |
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| 25 | 12 | Amber Herold | |
| 26 | 1 | Amber Herold | h3. Clustering by Affinity Propogation |
| 27 | 10 | Amber Herold | |
| 28 | * "Clustering by Passing Messages Between Data Points." (2007) Brendan J. Frey and Delbert Dueck. Science. v315(5814). PMID: 17218491 |
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| 29 | 1 | Amber Herold | |
| 30 | 12 | Amber Herold | h3. CTFFind |
| 31 | 10 | Amber Herold | |
| 32 | 1 | Amber Herold | * "Accurate determination of local defocus and specimen tilt in electron microscopy." (2003) Mindell, JA, Grigorieff N. J Struct Biol. v142(3). PMID: 12781660 |
| 33 | 10 | Amber Herold | |
| 34 | 12 | Amber Herold | h3. CTFTilt |
| 35 | 1 | Amber Herold | |
| 36 | 16 | Amber Herold | * 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 |
| 37 | 12 | Amber Herold | |
| 38 | h3. DogPicker |
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| 40 | 1 | Amber Herold | * "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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| 42 | 10 | Amber Herold | h3. EMAN |
| 43 | 4 | Amber Herold | |
| 44 | 1 | Amber Herold | * "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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| 46 | 12 | Amber Herold | h3. EM-BFACTOR |
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| 48 | h3. FindEM |
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| 50 | 10 | Amber Herold | h3. Frealign |
| 51 | 4 | Amber Herold | |
| 52 | 10 | Amber Herold | * "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 |
| 53 | 9 | Amber Herold | |
| 54 | 10 | Amber Herold | h3. IMAGIC |
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| 56 | 1 | Amber Herold | * "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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| 58 | 12 | Amber Herold | h3. IMOD |
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| 61 | h3. ProTomo |
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| 64 | h3. RMeasure |
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| 67 | 10 | Amber Herold | h3. SPIDER |
| 68 | 1 | Amber Herold | |
| 69 | * "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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| 70 | 12 | Amber Herold | |
| 71 | h3. TiltPicker |
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| 73 | 10 | Amber Herold | |
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| 75 | 5 | Amber Herold | h3. XMIPP |
| 76 | 9 | Amber Herold | |
| 77 | 6 | Amber Herold | * "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 |
| 78 | * "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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| 79 | * "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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| 80 | 9 | Amber Herold | * "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 |