PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis

Journal of Structural Biology

Volumn 178, Issue 2, 2012, Pages 177-188

  Hrabe, Thomas ^a   Chen, Yuxiang ^a   Pfeffer, Stefan ^a   Kuhn Cuellar, Luis ^a   Mangold, Ann Victoria ^a   Förster, Friedrich ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

Cryo electron tomography; Image processing; Software toolbox; Subtomogram analysis

Indexed keywords

ACCURACY; ALGORITHM; ANIMAL CELL; ARTICLE; CELL LYSATE; CELLULAR DISTRIBUTION; COMPUTER PROGRAM; CRYO ELECTRON TOMOGRAPHY; ELECTRON TOMOGRAPHY; MACROMOLECULE; NONHUMAN; PRIORITY JOURNAL; PYTOM; RIBOSOME; SIMULATION; STOCHASTIC MODEL; WORKFLOW; YEAST CELL;

ANIMALS; CRYOELECTRON MICROSCOPY; ELECTRON MICROSCOPE TOMOGRAPHY; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MACROMOLECULAR SUBSTANCES;

EID: 84860584901     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2011.12.003     Document Type: Article

References (47)

1. Adams P.D., Grosse-Kunstleve R.W., Hung L.W., Ioerger T.R., McCoy A.J., Moriarty N.W., Read R.J., Sacchettini J.C., Sauter N.K., Terwilliger T.C. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 2002, 58:1948-1954.
2. Amat F., Comolli L.R., Moussavi F., Smit J., Downing K.H., Horowitz M. Subtomogram alignment by adaptive Fourier coefficient thresholding. J. Struct. Biol. 2010, 171:332-344.
3. Bartesaghi A., Subramaniam S. Membrane protein structure determination using cryo-electron tomography and 3D image averaging. Curr. Opin. Struct. Biol. 2009, 19:402-407.
4. Bartesaghi A., Sprechmann P., Liu J., Randall G., Sapiro G., Subramaniam S. Classification and 3D averaging with missing wedge correction in biological electron tomography. J. Struct. Biol. 2008, 162:436-450.
5. Beck M., Malmstrom J.A., Lange V., Schmidt A., Deutsch E.W., Aebersold R. Visual proteomics of the human pathogen Leptospira interrogans. Nat. Methods 2009, 6:817-823.
6. Bohn S., Beck F., Sakata E., Walzthoeni T., Beck M., Aebersold R., Forster F., Baumeister W., Nickell S. Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution. Proc. Natl Acad. Sci. USA 2010, 107:20992-20997.
7. Brandt F., Carlson L.A., Hartl F.U., Baumeister W., Grunewald K. The three-dimensional organization of polyribosomes in intact human cells. Mol. Cell 2010, 39:560-569.
8. Brodsky J.L. The use of in vitro assays to measure endoplasmic reticulum-associated degradation. Methods Enzymol. 2010, 470:661-679.
9. Diday E. The dynamic clusters method in nonhierarchical clustering. Int. J. Comput. Inform. Sci. 1973, 2:61-88.
10. Duda R.O., Hart P.E., Stork D.G. Pattern Classification, second ed. 2000, Wiley, Interscience.
11. Fernandez J.J., Li S., Crowther R.A. CTF determination and correction in electron cryotomography. Ultramicroscopy 2006, 106:587-596.
12. Förster F., Hegerl R. Structure determination in situ by averaging of tomograms. Methods Cell Biol. 2007, 79:741-767.
13. Förster F., Han B.G., Beck M. Visual proteomics. Methods Enzymol. 2010, 483:215-243.
14. Förster F., Pruggnaller S., Seybert A., Frangakis A.S. Classification of cryo-electron sub-tomograms using constrained correlation. J. Struct. Biol. 2008, 161:276-286.
15. Förster F., Medalia O., Zauberman N., Baumeister W., Fass D. Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proc. Natl. Acad. Sci. USA 2005, 102:4729-4734.
16. Frangakis A.S., Forster F. Computational exploration of structural information from cryo-electron tomograms. Curr. Opin. Struct. Biol. 2004, 14:325-331.
17. Frangakis A.S., Böhm J., Förster F., Nickell S., Nicastro D., Typke D., Hegerl R., Baumeister W. Identification of macromolecular complexes in cryoelectron tomograms of phantom cells. Proc. Natl. Acad. Sci. USA 2002, 99:14153-14158.
18. Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., Leith A. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 1996, 116:190-199.
19. Grunewald K., Medalia O., Gross A., Steven A.C., Baumeister W. Prospects of electron cryotomography to visualize macromolecular complexes inside cellular compartments: implications of crowding. Biophys. Chem. 2003, 100:577-591.
20. Heumann J.M., Hoenger A., Mastronarde D.N. Clustering and variance maps for cryo-electron tomography using wedge-masked differences. J. Struct. Biol. 2011, 175:288-299.
21. Hohn M., Tang G., Goodyear G., Baldwin P.R., Huang Z., Penczek P.A., Yang C., Glaeser R.M., Adams P.D., Ludtke S.J. SPARX, a new environment for Cryo-EM image processing. J. Struct. Biol. 2007, 157:47-55.
22. Hrabe T., Förster F. Structure Determination by Single Particle Cryo-electron Tomography, eLS 2011, John Wiley & Sons Ltd.
23. Langlois R., Frank J. A clarification of the terms used in comparing semi-automated particle selection algorithms in Cryo-EM. J. Struct. Biol. 2011, 175:348-352.
24. Lucic V., Forster F., Baumeister W. Structural studies by electron tomography: from cells to molecules. Annu. Rev. Biochem. 2005, 74:833-865.
25. Ortiz J.O., Förster F., Kurner J., Linaroudis A.A., Baumeister W. Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition. J. Struct. Biol. 2006, 156:334-341.
26. Penczek P.A., Frank J., Spahn C.M. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol. 2006, 154:184-194.
27. Ramezani-Rad M., Käufer N.F., Hasilik A., Lochmann E. In vitro studies with rough microsomes from Saccharomyces cerevisiae. Endocyt. C. Res 1985, 2:249-260.
28. Rath B.K., Hegerl R., Leith A., Shaikh T.R., Wagenknecht T., Frank J. Fast 3D motif search of EM density maps using a locally normalized cross-correlation function. J. Struct. Biol. 2003, 144:95-103.
29. Renken C., Hsieh C.E., Marko M., Rath B., Leith A., Wagenknecht T., Frank J., Mannella C.A. Structure of frozen-hydrated triad junctions: a case study in motif searching inside tomograms. J. Struct. Biol. 2009, 165:53-63.
30. Roseman A.M. Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy 2003, 94:225-236.
31. Rosenthal P.B., Henderson R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 2003, 333:721-745.
32. Sali A., Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234:779-815.
33. Scheres S.H., Melero R., Valle M., Carazo J.M. Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization. Structure 2009, 17:1563-1572.
34. Scheres S.H., Nunez-Ramirez R., Sorzano C.O., Carazo J.M., Marabini R. Image processing for electron microscopy single-particle analysis using XMIPP. Nat. Protoc. 2008, 3:977-990.
35. Schmid M.F., Booth C.R. Methods for aligning and for averaging 3D volumes with missing data. J. Struct. Biol. 2008, 161:243-248.
36. Sorzano C.O., Bilbao-Castro J.R., Shkolnisky Y., Alcorlo M., Melero R., Caffarena-Fernandez G., Li M., Xu G., Marabini R., Carazo J.M. A clustering approach to multireference alignment of single-particle projections in electron microscopy. J. Struct. Biol. 2010, 171:197-206.
37. Sorzano C.O.S., Marabini R., Pascual-Montano A., Scheres S.H.W., Carazo J.M. Optimization problems in electron microscopy of single particles. Ann. Oper. Res. 2006, 148:133-165.
38. Stolken M., Beck F., Haller T., Hegerl R., Gutsche I., Carazo J.M., Baumeister W., Scheres S.H., Nickell S. Maximum likelihood based classification of electron tomographic data. J. Struct. Biol. 2010, 173:77-85.
39. Tang G., Peng L., Baldwin P.R., Mann D.S., Jiang W., Rees I., Ludtke S.J. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 2007, 157:38-46.
40. Walz J., Typke D., Nitsch M., Koster A.J., Hegerl R., Baumeister W. Electron tomography of single ice-embedded macromolecules: three-dimensional alignment and classification. J. Struct. Biol. 1997, 120:387-395.
41. Winkler H. 3D reconstruction and processing of volumetric data in cryo-electron tomography. J. Struct. Biol. 2007, 157:126-137.
42. Winkler H., Zhu P., Liu J., Ye F., Roux K.H., Taylor K.A. Tomographic subvolume alignment and subvolume classification applied to myosin V and SIV envelope spikes. J. Struct. Biol. 2009, 165:64-77.
43. Xu M., Beck M., Alber F. Template-free detection of macromolecular complexes in cryo electron tomograms. Bioinformatics 2011, 27:i69-i76.
44. Yu L., Snapp R.R., Ruiz T., Radermacher M. Probabilistic principal component analysis with expectation maximization (PPCA-EM) facilitates volume classification and estimates the missing data. J. Struct. Biol. 2010.
45. Yu Z., Frangakis A.S. Classification of electron sub-tomograms with neural networks and its application to template-matching. J. Struct. Biol. 2011, 174:494-504.
46. Zanetti G., Riches J.D., Fuller S.D., Briggs J.A. Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging. J. Struct. Biol. 2009, 168:305-312.
47. Zsigmondy, R., Thiessen, P.A., 1925. Das Kolloid Gold Akademischer Verlag, Leipzig.