Detecting consistent common lines in cryo-EM by voting

Journal of Structural Biology

Volumn 169, Issue 3, 2010, Pages 312-322

  Singer, Amit ^a   Coifman, Ronald R ^b   Sigworth, Fred J ^c   Chester, David W ^c   Shkolnisky, Yoel ^d  

^a PRINCETON UNIVERSITY   (United States)

^b YALE UNIVERSITY   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d TEL AVIV UNIVERSITY   (Israel)

Author keywords

Angular reconstitution; Bayesian approach; Common lines; Cryo electron microscopy; Single particle reconstruction

Indexed keywords

ALGORITHM; ARTICLE; CRYOELECTRON MICROSCOPY; ESCHERICHIA COLI; FOURIER ANALYSIS; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; RIBOSOME SUBUNIT; SIMULATION;

ALGORITHMS; BAYES THEOREM; CRYOELECTRON MICROSCOPY; FOURIER ANALYSIS; IMAGE PROCESSING, COMPUTER-ASSISTED;

EID: 76749144632     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2009.11.003     Document Type: Article

References (24)

1. Ban N., Nissen P., Hansen J., Moore P.B., and Steitz T.A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289 (2000) 905-920
2. Chiu W., Baker L.M., Jiang W., Dougherty M., and Schmid M.F. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 13 3 (2005) 363-372 Review. PMID: 15766537 [PubMed - indexed for MEDLINE]
3. Coifman, R.R., Shkolnisky, Y., Sigworth, F.J., Singer, A., 2009. Reference free structure determination through eigenvectors of center of mass operators. Applied and Computational Harmonic Analysis, in press, doi:10.1016/j.acha.2009.11.003.
4. Farrow M., and Ottensmeyer P. A posteriori determination of relative projection directions of arbitrarily oriented macromolecules. Journal of the Optical Society of America A: Optics, Image Science, and Vision 9 10 (1992) 1749-1760
5. Frank J. Three-dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in their Native State (2006), Oxford
6. Golub G.H., and Van Loan C.F. Matrix Computation. Johns Hopkins Series in the Mathematical Sciences (1984), The Johns Hopkins University Press
7. Goncharov A.B. Integral geometry and three-dimensional reconstruction of randomly oriented identical particles from their electron microphotos. Acta Applicandae Mathematicae 11 (1988) 199-211
8. Henderson R. Realizing the potential of electron cryo-microscopy. Quarterly Reviews of Biophysics 37 1 (2004) 3-13 Review. PMID: 17390603 [PubMed - indexed for MEDLINE]
9. Ludtke S.J., Baker M.L., Chen D.H., Song J.L., Chuang D.T., and Chiu W. De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16 3 (2008) 441-448
10. Mallick S.P., Agarwal S., Kriegman D.J., Belongie S.J., Carragher B., and Potter C.S. Structure and view estimation for tomographic reconstruction: a Bayesian approach. Computer Vision and Pattern Recognition (CVPR) II (2006) 2253-2260
11. Natterer F. The Mathematics of Computerized Tomography. Classics in Applied Mathematics (2001), SIAM: Society for Industrial and Applied Mathematics
12. Penczek P.A., Grassucci R.A., and Frank J. The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy 53 (1994) 251-270
13. Penczek P.A., Zhu J., and Frank J. A common-lines based method for determining orientations for N > 3 particle projections simultaneously. Ultramicroscopy 63 (1996) 205-218
14. Salzman D.B. A method of general moments for orienting 2D projections of unknown 3D objects. Computer Vision, Graphics, and Image Processing 50 (1990) 129-156
15. Serysheva I.I., Orlova E.V., Chiu W., Sherman M.B., Hamilton S.L., and van Heel M. Electron cryomicroscopy and angular reconstitution used to visualize the skeletal muscle calcium release channel. Nature Structural Biology 2 (1995) 18-24
16. Stark H., Rodnina M.V., Wieden H.J., Zemlin F., Wintermeyer W., and van Heel M. Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex. Nature Structural Biology 9 (2002) 849-854
17. Vainshtein, B., Goncharov, A., 1986. Determination of the spatial orientation of arbitrarily arranged identical particles of an unknown structure from their projections. In: Proc. 11th Intern. Congr. on Elec. Mirco. pp. 459-460.
18. van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy 21 2 (1987) 111-123 PMID: 12425301 [PubMed - indexed for MEDLINE]
19. Van Heel M., Orlova E.V., Harauz G., Stark H., Dube P., and Zemlin F.M.S. Angular reconstitution in three-dimensional electron microscopy: historical and theoretical aspects. Scanning Microscopy 11 (1997) 195-210
20. van Heel M., Harauz G., Orlova E.V., Schmidt R., and Schatz M. A new generation of the IMAGIC image processing system. Journal of Structural Biology 116 1 (1996) 17-24
21. Wang L., and Sigworth F.J. Cryo-em and single particles. Physiology (Bethesda) 21 (2006) 13-18 Review. PMID: 16443818 [PubMed - indexed for MEDLINE]
22. Zakai M., and Ziv J. On the threshold effect in radar range estimation. IEEE Transactions on Information Theory 15 1 (1969) 167-170
23. Zhang X., Settembre E., Xu C., Dormitzer P.R., Bellamy R., Harrison S.C., and Grigorieff N. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proceedings of the National Academy of Sciences 105 6 (2008) 1867-1872
24. Ziv J., and Zakai M. Some lower bounds on signal parameter estimation. IEEE Transactions on Information Theory 15 3 (1969) 386-391