Appion citations » History » Version 29
Bridget Carragher, 01/30/2011 01:53 PM
| 1 | 11 | Amber Herold | h1. Appion Citations |
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| 2 | 1 | Amber Herold | |
| 3 | 29 | Bridget Carragher | Appion includes software from the following packages (more information on most of these packages can be found in the "Wikibook":http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy describing EM software packages): |
| 4 | 2 | Amber Herold | |
| 5 | |||
| 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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| 14 | |||
| 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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| 21 | |||
| 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 |
| 24 | |||
| 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 | 17 | 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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| 39 | |||
| 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 | 24 | Amber Herold | h3. Ed's Iteration Alignment |
| 43 | |||
| 44 | * "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 |
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| 45 | |||
| 46 | 10 | Amber Herold | h3. EMAN |
| 47 | 4 | Amber Herold | |
| 48 | 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 |
| 49 | |||
| 50 | 12 | Amber Herold | h3. EM-BFACTOR |
| 51 | |||
| 52 | 18 | Amber Herold | * "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. |
| 53 | 19 | Amber Herold | * "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 |
| 54 | 18 | Amber Herold | |
| 55 | 12 | Amber Herold | h3. FindEM |
| 56 | |||
| 57 | 20 | Amber Herold | * "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 |
| 58 | * Roseman, 2003. A.M. Roseman, Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy 94 (2003), pp. 225–236. |
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| 59 | |||
| 60 | 10 | Amber Herold | h3. Frealign |
| 61 | 4 | Amber Herold | |
| 62 | 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 |
| 63 | 9 | Amber Herold | |
| 64 | 10 | Amber Herold | h3. IMAGIC |
| 65 | |||
| 66 | 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 |
| 67 | |||
| 68 | 12 | Amber Herold | h3. IMOD |
| 69 | |||
| 70 | 21 | Amber Herold | * 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 |
| 71 | 28 | Amber Herold | * "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 |
| 72 | 12 | Amber Herold | |
| 73 | h3. ProTomo |
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| 74 | 21 | Amber Herold | |
| 75 | * "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. |
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| 76 | * "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. |
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| 77 | * "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. |
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| 78 | * "3D reconstruction and processing of volumetric data in cryo-electron tomography" H. Winkler, J. Struct. Biol. 157, 126-137, 2007. |
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| 79 | 12 | Amber Herold | |
| 80 | |||
| 81 | h3. RMeasure |
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| 82 | |||
| 83 | 22 | Amber Herold | * Sousa, D, Grigorieff N. 2007. Ab initio resolution measurement for single particle structures. J Struct Biol. 157:201-10. |
| 84 | 12 | Amber Herold | |
| 85 | 25 | Amber Herold | h3. SIGNATURE |
| 86 | |||
| 87 | * "SIGNATURE: a single-particle selection system for molecular electron microscopy." (2007) Chen JZ, Grigorieff N., J Struct Biol. v.157(1) PMID: 16870473 |
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| 88 | |||
| 89 | 10 | Amber Herold | h3. SPIDER |
| 90 | 1 | Amber Herold | |
| 91 | * "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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| 92 | 12 | Amber Herold | |
| 93 | h3. TiltPicker |
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| 94 | |||
| 95 | 23 | Amber Herold | * 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. |
| 96 | 26 | Amber Herold | |
| 97 | |||
| 98 | 27 | Amber Herold | h3. Topology Alignment |
| 99 | |||
| 100 | * "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., v.143(3) PMID: 14572474 |
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| 101 | |||
| 102 | 5 | Amber Herold | h3. XMIPP |
| 103 | 9 | Amber Herold | |
| 104 | 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 |
| 105 | * "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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| 106 | * "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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| 107 | 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 |