Gradient-based high precision alignment of cryo-electron subtomograms

2011 IEEE International Conference on Systems Biology, ISB 2011

Volumn , Issue , 2011, Pages 279-284

  Xu, Min ^a   Alber, Frank ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT METHODS; CRYO-ELECTRON TOMOGRAPHY; GRADIENT BASED; HIGH PRECISION; INITIAL ALIGNMENT; LIVING CONDITIONS; LOW RESOLUTION; LOW SIGNAL-TO-NOISE RATIO; MACROMOLECULAR COMPLEXES; MISSING DATA; MODEL COMPLEXES; PARALLEL OPTIMIZATION; PROTEIN COMPLEXES; RELATIVE ROTATION; SIMILARITY MEASURE; SIMULATED DATA; STRUCTURAL CHARACTERIZATION; STRUCTURAL SYSTEMS; WHOLE CELL;

BIOLOGY; COMPUTER SIMULATION; ELECTRIC IMPEDANCE TOMOGRAPHY; SIGNAL TO NOISE RATIO;

ALIGNMENT;

EID: 80054874844     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ISB.2011.6033166     Document Type: Conference Paper

References (18)

1. S. Kühner, V. Van Noort, M. Betts, A. Leo-Macias, C. Batisse, M. Rode, T. Yamada, T. Maier, S. Bader, P. Beltran-Alvarez et al., "Proteome organization in a genome-reduced bacterium", Science, vol. 326, no. 5957, p. 1235, 2009.
2. N. Gehlenborg, S. O'Donoghue, N. Baliga, A. Goesmann, M. Hibbs, H. Kitano, O. Kohlbacher, H. Neuweger, R. Schneider, D. Tenenbaum et al., "Visualization of omics data for systems biology", Nat Methods, vol. 7, no. 3 Suppl, pp. S56-68, 2010.
3. S. Nickell, C. Kofler, A. Leis, and W. Baumeister, "A visual approach to proteomics", Nature reviews Molecular cell biology, vol. 7, no. 3, pp. 225-230, 2006.
4. M. Beck, J. Malmström, V. Lange, A. Schmidt, E. Deutsch, and R. Aebersold, "Visual proteomics of the human pathogen Leptospira interrogans", Nature methods, vol. 6, no. 11, pp. 817-823, 2009.
5. M. Beck, M. Topf, Z. Frazier, H. Tjong, M. Xu, S. Zhang, and F. Alber, "Exploring the Spatial and Temporal Organization of a Cell's Proteome", Journal of Structural Biology, vol. 173, no. 3, pp. 483-496, 2011.
6. M. Xu, M. Beck, and F. Alber, "Template-free detection of macromolecular complexes in cryo electron tomograms", Bioinformatics, 2011.
7. F. Förster, O. Medalia, N. Zauberman, W. Baumeister, and D. Fass, "Retrovirus envelope protein complex structure in situ studied by cryoelectron tomography", Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 13, p. 4729, 2005.
8. V. Martin Beck et al., "Snapshots of nuclear pore complexes in action captured by cryo-electron tomography", Nature, vol. 449, no. 7162, pp. 611-615, 2007.
9. F. Förster, S. Pruggnaller, A. Seybert, and A. Frangakis, "Classification of cryo-electron sub-tomograms using constrained correlation", Journal of structural biology, vol. 161, no. 3, pp. 276-286, 2008.
10. F. Amat, L. Comolli, F. Moussavi, J. Smit, K. Downing, and M. Horowitz, "Subtomogram alignment by adaptive Fourier coefficient thresholding", Journal of structural biology, 2010.
11. A. Bartesaghi, P. Sprechmann, J. Liu, G. Randall, G. Sapiro, and S. Subramaniam, "Classification and 3D averaging with missing wedge correction in biological electron tomography", Journal of structural biology, vol. 162, no. 3, pp. 436-450, 2008.
12. D. Brink and G. Satchler, Angular momentum. Oxford University Press, USA, 1993.
13. J. Nocedal and S. Wright, Numerical optimization. Springer, Berlin, 2006.
14. S. Nickell, F. Förster, A. Linaroudis, W. Net, F. Beck, R. Hegerl, W. Baumeister, and J. Plitzko, "TOM software toolbox: acquisition and analysis for electron tomography", Journal of Structural Biology, vol. 149, no. 3, pp. 227-234, 2005.
15. J. Frank, Three-dimensional electron microscopy of macromolecular assemblies: visualization of biological molecules in their native state. Oxford University Press, USA, 2006.
16. G. McMullan, S. Chen, R. Henderson, and A. Faruqi, "Detective quantum efficiency of electron area detectors in electron microscopy", Ultramicroscopy, vol. 109, no. 9, pp. 1126-1143, 2009.
17. E. Pettersen, T. Goddard, C. Huang, G. Couch, D. Greenblatt, E. Meng, and T. Ferrin, "UCSF Chimeraa visualization system for exploratory research and analysis", Journal of computational chemistry, vol. 25, no. 13, pp. 1605-1612, 2004.
18. W. Wriggers, R. Milligan, and J. McCammon, "Situs: A Package for Docking Crystal Structures into Low-Resolution Maps from Electron Microscopy", Journal of Structural Biology, vol. 125, no. 2-3, pp. 185-195, 1999.