Volumetric restrictions in single particle 3DEM reconstruction

Pattern Recognition

Volumn 41, Issue 2, 2008, Pages 616-626

  Sorzano, C O S ^a,b   Velazquez Muriel J A ^a   Marabini, R ^c   Herman, G T ^d   Carazo, J M ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b UNIVERSIDAD SAN PABLO CEU   (Spain)

^c UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^d CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

Constrained reconstruction; Electron microscopy; Single particles; Tomography

Indexed keywords

ANGULAR DISTRIBUTION; CONSTRAINED OPTIMIZATION; ELECTRON MICROSCOPY; ELECTROSTATIC PRECIPITATORS; MACROMOLECULES; THREE DIMENSIONAL COMPUTER GRAPHICS;

DENSITY NONNEGATIVITY; MOLECULE FLEXIBILITY; PARTICLE SYMMETRY;

IMAGE RECONSTRUCTION;

EID: 34848890896     PISSN: 00313203     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.patcog.2007.06.010     Document Type: Article

References (29)

1. Agirrezabala X., Martín-Benito J., Valle M., González J.M., Valencia A., Valpuesta J.M., and Carrascosa J.L. Structure of the connector of T7 bacteriophage at 8 over(A, ̊) resolution: structural homologies of a basic component of a dna translocating machinery. J. Mol. Biol. 347 (2005) 895-902
2. Clare D.K., Bakkes P.J., van Heerikhuizen H., van der Vies S.M., and Saibil H.R. An expanded protein folding cage in the groel-gp31 complex. J. Mol. Biol. 358 (2006) 905-911
3. Halic M., Becker T., Frank J., Spahn C.M., and Becjmann R. Localization and dynamic behavior of ribosomal protein L30e. Nat. Struct. Mol. Biol. 12 (2005) 467-468
4. Ludtke S.J., Chen D.H., Song J.L., Chuang D.T., and Chiu W. Seeing GroEL at 6 over(A, ̊) resolution by single particle electron cryomicroscopy. Structure 12 (2004) 1129-1136
5. Schmid M.F., Sherman M.B., Matsudaira P., and Chiu W. Structure of the acrosomal bundle. Nature 431 (2004) 104-107
6. Valle M., Zavialov A., Li W., Stagg S., Sengupta J., Nielsen R., Nissen P., Harvey S., Ehrenberg M., and Frank J. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat. Struct. Biol. 10 (2003) 899-906
7. Zheng Y., Doerschuk P., and Johnson J. Symmetry-constrained 3D interpolation of viral X-ray crystallography data. IEEE Trans. Signal Process. 48 (2000) 214-222
8. Marabini R., Herman G.T., and Carazo J.M. 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). Ultramicroscopy 72 (1998) 53-65
9. Carazo J.M. The fidelity of 3D reconstructions from incomplete data and the use of restoration methods. In: Frank J. (Ed). Electron Tomography. Three-Dimensional Imaging with the Transmission Electron Microscope (1992), Plenum Press, New York 117-166
10. Sezan M.I., and Stark H. Image restoration by convex projections in the presence of noise. Appl. Opt. 22 (1983) 2781-2789
11. Stark H., and Peng H. Shape estimation in computer tomography from minimal data. J. Opt. Soc. Am. A 5 (1988) 331-343
12. Yeh S.J., and Stark H. Iterative and one-step reconstruction from nonuniform samples by convex projections. J. Opt. Soc. Am. A 7 (1990) 491-499
13. Lewitt R.M. Multidimensional digital image representations using generalized Kaiser-Bessel window functions. J. Opt. Soc. Am. A 7 (1990) 1834-1846
14. Eggermont P.P.B., Herman G.T., and Lent A. Iterative algorithms for large partitioned linear systems with applications to image reconstruction. Linear Algebra Appl. 40 (1981) 37-67
15. Herman G.T. Image Reconstruction from Projections: The Fundamentals of Computerized Tomography (1980), Academic Press, New York
16. Fuchs K.G., Tittmann P., Krusche K., and Gross H. Reconstruction and representation of surface data from two-dimensional crystalline biological macromolecules. Bioimaging 3 (1995) 12-24
17. Engel A., and Muller D.J. Observing single biomolecules at work with the atomic force microscope. Nat. Struct. Biol. 7 (2000) 715-718
18. Sorzano C.O.S., Marabini R., Herman G.T., and Carazo J.M. Volumetric constraints in 3D tomography applied to electron microscopy. Proceedings of the 1st International Symposium on Biomedical Imaging, Washington, USA (2002) 641-644
19. Sorzano C.O.S., de la Fraga L.G., Clackdoyle R., and Carazo J.M. Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy. Ultramicroscopy 101 (2004) 129-138
20. Bárcena M., Donate L., Ruiz T., Dixon N., Radermacher M., and Carazo J.M. The DnaB-DnaC complex: a structure based on interactions among assymetric dimers. EMBO J. 20 (2001) 1462-1468
21. Ceska T.A., Henderson R., Baldwin J.M., Zemlin F., Beckmann E., and Downing K. An atomic model for the structure of bacteriorhodopsin, a seven-helix membrane protein. Acta Physiol. Scand. Suppl. 607 (1992) 31-40
22. Sorzano C.O.S., Marabini R., Boisset N., Rietzel E., Schröder R., Herman G.T., and Carazo J.M. The effect of overabundant projection directions on 3D reconstruction algorithms. J. Struct. Biol. 133 (2001) 108-118
23. Frank J. Three Dimensional Electron Microscopy of Macromolecular Assemblies (1996), Academic Press, San Diego, CA
24. Velázquez-Muriel J.A., Sorzano C.O.S., Fernández J.J., and Carazo J.M. A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjusting. Ultramicroscopy 96 (2003) 17-35
25. Unser M., Sorzano C.O.S., Thévenaz P., Jonic S., El-Bez C., De Carlo S., Conway J., and Trus B.L. Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions. J. Struct. Biol. 149 (2005) 243-255
26. Pratt W.K. Digital Image Processing. second ed. (1991), Wiley-Interscience, New York
27. Peng H., and Stark H. One-step image reconstruction from incomplete data in computer tomography. IEEE Trans. Med. Imag. 8 (1989) 16-31
28. Wang B.C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115 (1985) 90-112
29. Lee I. Curve reconstruction from unorganized points. Comput. Aided Geom. Des. 17 (2000) 161-177