Automatic structure interpretation of single particle cryo-electron microscopy: From images to psuedo-atomic models

2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings

Volumn , Issue , 2007, Pages 236-239

  Bajaj, Chandrajit L ^a  

^a University of Texas at Austin   (United States)

Author keywords

Biomedical microscopy; Biomedical signal processing; Computational geometry; Computer aided analysis

Indexed keywords

BIOMEDICAL MICROSCOPY; BIOMEDICAL SIGNAL PROCESSING; MOLECULAR DOMAIN SEGMENTATION; PROTEIN SECONDARY STRUCTURES;

COMPUTATIONAL GEOMETRY; COMPUTER AIDED ANALYSIS; IMAGE RECONSTRUCTION; IMAGE SEGMENTATION; MACROMOLECULES; PROTEINS;

ELECTRON MICROSCOPY;

EID: 36348977502     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ISBI.2007.356832     Document Type: Conference Paper

References (22)

1. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne, "The protein data bank," Nucleic Acids Research, vol. 28, pp. 235-242, 2000.
2. S.J. Ludtke, P.R. Baldwin, and W. Chiu, "EMAN: semiautomated software for high-resolution single-particle reconstructions," Journal of Structural Biology, vol. 128, pp. 82-97, 1999.
3. J. Frank, M. Radermacher, P. Penczek, J. Zhu, Y. Li, M. Ladjadj, and A. Leith, "SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields," Journal of Structural Biology, vol. 116, pp. 190-199, 1996.
4. M. Van Heel, G. Harauz, E.V. Orlova, R. Schmidt, and M. Schatz, "A new generation of the IMAGIC image processing system," Journal of Structural Biology, vol. 116, pp. 17-24, 1996.
5. W. Jiang, Z. Li, M. L. Baker, P. E. Prevelige, and W. Chiu, "Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolution," Nature Structural Biology, vol. 10, no. 2, pp. 131-135, 2003.
6. T. S. Baker, N. H. Olson, and S. D. Fuller, "Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs," Microbiology and Molecular Biology Reviews, vol. 63, no. 4, pp. 862-922, 1999.
7. " IEEE Transactions on Image Processing: Special Issue on Molecular and Cellular Bioimaging (Guest Editors: R.F. Murphy, E. Meijering and G. Danuser), vol. 14, no. 9, 2005.
8. Z. Yu and C. Bajaj, "Automatic ultra-structure segmentation of reconstructed cryo-em maps of icosahedral viruses," IEEE Transactions on Image Processing, vol. 14, no. 9, pp. 1324-1337, 2005.
9. M. Baker, Z. Yu, W. Chiu, and C. Bajaj, "Automated segmentation of molecular subunits in electron cryomicroscopy density maps," Journal of Structural Biology, vol. 156, no. 3, pp. 432-441, 2006.
10. J. Weickert, Anisotropic Diffusion In Image Processing, ECMI Series, Teubner, Stuttgart, ISBN 3-519-02606-6, 1998.
11. C. Bajaj, Q. Wu, and G. Xu, "Volumetric anisotropic diffusion for 3d image denoising," Tech. Rep. ICES Tech Rep 02-27, The University of Texas at Austin, 2002.
12. C. Xu and J. L. Prince, "Snakes, shapes, and gradient vector flow," IEEE Trans. Image Processing, vol. 7, no. 3, pp. 359-369, 1998.
13. Z. Yu and C. Bajaj, "Anisotropic vector diffusion in image smoothing," in Proceeding of the 9th IEEE ICIP, 2002, vol. 1, pp. 828-831.
14. Z. Yu and C. Bajaj, "Image segmentation using gradient vector diffusion and region merging," in International Conference on Pattern Recognition, 2002, pp. 941-944.
15. N. Volkmann, "A novel three-dimensional variant of the watershed transform for segmentation of electron density maps," Journal of Structural Biology, vol. 138(1 -2), pp. 123-129, 2002.
16. A. S. Frangakis and R. Hegerl, "Segmentation of twoand three-dimensional data from electron microscopy using eigenvector analysis," Journal of Structural Biology, vol. 138(1-2), pp. 105-113, 2002.
17. R. Malladi and J. A. Sethian, "A real-time algorithm for medical shape recovery," in Proc. of Int'l Conf. on Computer Vision, 1998, pp. 304-310.
18. C. Branden and J. Tooze, An Introduction to Protein Structure, Garland Publishing Inc., New York, 1999.
19. J. Wen, M. Baker, S. Ludtke, and W. Chiu, "Bridging the information gap: computational tools for intermediate resolution structure interpretation," J. of Mol. Bio., vol. 308, pp. 1033-1044, 2001.
20. Y. Kong, X.Zhang, T.S.Baker, and J. Ma, "A structuralinformatics approach for tracing b-sheets: building pseudo-ca traces for b-strands in intermediate-resolution density maps," Journal of Molecular Biology, vol. 339, pp. 117-130, 2004.
21. Z. Yu and C. Bajaj, "Computational approaches for automatic structural analysis of large bio-molecular complexes," Tech. Rep. TR-06-05, Department of Computer Sciences, UT Austin, 2006.
22. C. Bajaj and S. Goswami, "Automatic fold and structural motif elucidation from 3D EM maps of macromolecules," in ICVGIP 2006, LNCS 4338, 2006, pp. 264-275.