Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs

Journal of Structural Biology

Volumn 178, Issue 2, 2012, Pages 121-128

  Rusu, Mirabela ^a,f   Starosolski, Zbigniew ^b,c   Wahle, Manuel ^a   Rigort, Alexander ^d   Wriggers, Willy ^e  

^a UNIVERSITY OF TEXAS   (United States)

^b SILESIAN UNIVERSITY OF TECHNOLOGY   (Poland)

^c TEXAS CHILDREN S HOSPITAL   (United States)

^d MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^e WEILL CORNELL MEDICAL COLLEGE   (United States)

^f RUTGERS UNIVERSITY   (United States)

Author keywords

3D analysis; Actin networks; Denoising; Filament detection; Segmentation; Tomograms

Indexed keywords

ACTIN;

ACTIN FILAMENT; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; CROSS LINKING; ELECTRON TOMOGRAPHY; GENETIC ALGORITHM; PRIORITY JOURNAL; REPRODUCIBILITY; STOCHASTIC MODEL; WORKFLOW;

ALGORITHMS; CRYOELECTRON MICROSCOPY; CYTOSKELETON; ELECTRON MICROSCOPE TOMOGRAPHY; MODELS, MOLECULAR; SOFTWARE;

EID: 84860577952     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2012.03.001     Document Type: Article

References (26)

1. Baumeister W. Electron tomography: towards visualizing the molecular organization of the cytoplasm. Curr. Opin. Struct. Biol. 2002, 12:679-684.
2. Birmanns S., Rusu M., Wriggers W. Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes. J. Struct. Biol. 2011, 173:428-435.
3. Birmanns S., Wriggers W. Interactive fitting augmented by force-feedback and virtual reality. J. Struct. Biol. 2003, 144:123-131.
4. Briggs J.A., Grünewald K., Glass B., Förster F., Kräusslich H.G., et al. The mechanism of HIV-1 core assembly: insights from three-dimensional reconstructions of authentic virions. Structure 2007, 14:15-20.
5. Chacón P., Wriggers W. Multi-resolution contour-based fitting of macromolecular structures. J. Mol. Biol. 2002, 317:375-384.
6. Frangakis A.S., Förster F. Computational exploration of structural information from cryo-electron tomograms. Curr. Opin. Struct. Biol. 2004, 14:325-331.
7. Frangakis A.S., Hegerl R. Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 2001, 135:239-250.
8. Goldberg D.E. Genetic Algorithms in Search, Optimization, and Machine Learning 1989, Addison-Wesley, Reading, MA.
9. Medalia O., Beck M., Ecke M., Weber I., Neujahr R., et al. Organization of actin networks in intact filopodia. Curr. Biol. 2007, 17:79-84.
10. Medalia O., Weber I., Frangakis A.S., Nicastro D., Gerisch G., et al. Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 2002, 298:1209-1213.
11. Narasimha R., Aganj I., Bennett A.E., Borgnia M.J., Zabransky D., et al. Evaluation of denoising algorithms for biological electron tomography. J. Struct. Biol. 2008, 164:7-17.
12. Penczek P., Frank J. Resolution in electron tomography. Electron Tomography 2006, 307-330. Springer-Verlag, New York. J. Frank (Ed.).
13. Pollard T., Beltzner C.C. Structure and function of the Arp2/3 complex. Curr. Opin. Struct. Biol. 2002, 12:768-774.
14. Pollard T.D., Borisy G.G. Cellular motility driven by assembly and disassembly of actin filaments. Cell 2003, 112:453-465.
15. Radermacher M. Three-dimensional reconstruction of single particles from random and nonrandom tilt series. J. Electron Microsc. Tech. 1988, 9:359-394.
16. Radermacher M. Weighted Back-Projections Methods 1992, Plenum Press, New York.
17. Rigort A., Günther D., Hegerl R., Baum D., Weber B., et al. Automated segmentation of electron tomograms for a quantitative description of actin filament networks. J. Struct. Biol. 2012, 177:135-144.
18. Rusu M., Birmanns S. Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. J. Struct. Biol. 2010, 170:164-171.
19. Rusu M., Wriggers W. Evolutionary bidirectional expansion for the annotation of alpha helices in cryo-electron microscopy reconstructions 2012, 177:410-419.
20. Smolka B. Peer group filter for impulsive noise removal in color images. IEEE Trans. Med. Imaging 2008, 27:699-707.
21. Stoschek A., Hegerl R. Denoising of electron tomographic reconstructions using multiscale transformations. J. Struct. Biol. 1997, 120:257-265.
22. Szczepanski M., Smolka B., Plataniotis K., Venetsanopoulos A. On the distance function approach to color image enhancement. Discrete Appl. Math. 2004, 139:283-305.
23. Volkmann N. A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. J. Struct. Biol. 2002, 138:123-129.
24. Weber B., Greenan G., Prohaska S., Baum D., Hege H.-C., et al. Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos. J. Struct. Biol. 2012, 178:129-138.
25. Wriggers W. Using Situs for the integration of multi-resolution structures. Biophys. Rev. 2010, 2:21-27.
26. Wriggers W., Milligan R.A., McCammon J.A. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 1999, 125:185-195.