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Appion Citations

Appion includes software from the following packages (more information on most of these packages can be found in the Wikibook describing EM software packages):

ACE

  • "ACE: automated CTF estimation." (2005) Mallick SP, Carragher B, Potter CS, Kriegman DJ. Ultramicroscopy. v104(1). PMID: 15935913

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

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

Chimera

Clustering by Affinity Propogation

  • "Clustering by Passing Messages Between Data Points." (2007) Brendan J. Frey and Delbert Dueck. Science. v315(5814). PMID: 17218491

CTFFind

  • "Accurate determination of local defocus and specimen tilt in electron microscopy." (2003) Mindell, JA, Grigorieff N. J Struct Biol. v142(3). PMID: 12781660

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

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

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

EMAN

  • "EMAN: semiautomated software for high-resolution single-particle reconstructions." (1999) Ludtke SJ, Baldwin PR, Chiu W. J Struct Biol. v128(1). PMID: 10600563

EM-BFACTOR

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.

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

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

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
  • "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

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.

RMeasure

  • Sousa, D, Grigorieff N. 2007. Ab initio resolution measurement for single particle structures. J Struct Biol. 157:201-10.

SIGNATURE

  • "SIGNATURE: a single-particle selection system for molecular electron microscopy." (2007) Chen JZ, Grigorieff N., J Struct Biol. v.157(1) PMID: 16870473

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

TiltPicker

Topology 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., v.143(3) PMID: 14572474

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

Updated by Bridget Carragher about 13 years ago · 29 revisions