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Avoiding Local Optima in Single Particle Reconstruction

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Research in Computational Molecular Biology (RECOMB 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3500))

Abstract

In single-particle reconstruction, a 3D structure is reconstructed from a large number of randomly oriented 2D projections, using techniques related to computed tomography. Unlike in computed tomography, however, the orientations of the projections must be estimated at the same time as the 3D structure, and hence the reconstruction process can be error-prone, converging to an incorrect local optimum rather than the true 3D structure. In this paper, we discuss and further develop a maximum-likelihood approach to reconstruction, and demonstrate that this approach can help avoid incorrect local optima for both 2D and 3D reconstructions.

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References

  1. Abbott, A.: The society of proteins. Nature 417, 894–896 (2002)

    Article  Google Scholar 

  2. Brown, L.G.: A survey of image registration techniques. ACM Computing Surveys 24, 325–376 (1992)

    Article  Google Scholar 

  3. Dempster, A., Laird, N., Rubin, D.: Maximum likelihood from incomplete data via the EM algorithm (with discussion). J. Royal Statistical Soc. B 39, 1–38 (1977)

    MATH  MathSciNet  Google Scholar 

  4. Efron, B.: The Jackknife, the Bootstrap and Other Resampling Plans. CBMS-NSF Regional Conference Series in Applied Mathematics, vol. 38. SIAM, Philadelphia (1982)

    Google Scholar 

  5. Frank, J.: Three-dimensional electron microscopy of macromolecular assemblies. Academic Press, London (1996)

    Google Scholar 

  6. Frank, J., Radermacher, M., Penczek, P., Zhu, J., Li, Y., Ladjadj, M., Leith, A.: SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996), http://www.wadsworth.org/spider_doc/spider/docs/

    Article  Google Scholar 

  7. Hastie, T., Tibshirani, R., Friedman, J.: The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Springer, Heidelberg (2001)

    MATH  Google Scholar 

  8. Kirkpatrick, S., Gelatt, C.D., Vecchi, M.P.: Optimization by simulated annealing. Science 220, 671–680 (1983)

    Article  MathSciNet  Google Scholar 

  9. Koster, A.J., Grimm, R., Typke, D., Hegerl, R., Stoschek, A., Walz, J., Baumeister, W.: Perspectives of molecular and cellular electron tomography. J. Struct. Biology 120, 276–308 (1997)

    Article  Google Scholar 

  10. Ludtke, S.J., Baldwin, P.R., Chiu, W.: EMAN: Semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97 (1999), http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/doc/home.html

    Article  Google Scholar 

  11. Orlova, E.V., Dube, P., Harris, J.R., Beckman, E., Zemlin, F., Markl, J.: Structure of keyhole limpet hemocyanin type 1 (KLH1) at 15 Å resolution by electron cryomicroscopy and angular reconstitution. J. Molecular Biology 271, 417–437 (1997)

    Article  Google Scholar 

  12. Penczek, P., Radermacher, M., Frank, J.: Three-dimensional reconstruction of single particles embedded in ice. Ultramicroscopy 40, 33–53 (1992)

    Article  Google Scholar 

  13. Rouiller, I., DeLaBarre, B., May, A.P., Weis, W.I., Brunger, A.T., Milligan, R., Wilson-Kubalek, E.M.: Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle. Nature Struct. Biol. 9, 950–957 (2002)

    Article  Google Scholar 

  14. Ruprecht, J., Nield, J.: Determining the structure of biological macromolecules by transmission electron microscopy, single particle analysis and 3D reconstruction. Progress in Biophysics and Molecular Biology 75, 121–164 (2001)

    Article  Google Scholar 

  15. Saxton, W.O., Frank, J.: Motif detection in quantum noise-limited electron micrographs by cross-correlation. Ultramicroscopy 2, 219–227 (1977)

    Article  Google Scholar 

  16. Sigworth, F.J.: A maximum-likelihood approach to single-particle image refinement. J. Struct. Biology 122, 328–339 (1998)

    Article  Google Scholar 

  17. Stark, H.: 3D Electron Cryomicroscopy, http://www.mpibpc.gwdg.de/abteilungen/103/index.html

  18. van Heel, M., et al.: Single-particle electron microscopy: towards atomic resolution. Quarterly Reviews of Biophysics 33, 307–369 (2000)

    Article  Google Scholar 

  19. Wong, H.C., Chen, J., Mouche, F., Rouiller, I., Bern, M.: Model-based particle picking for cryo-electron microscopy. J. Struct. Biology 145, 157–167 (2004)

    Article  Google Scholar 

  20. Yonekura, K., Maki-Yonekura, S., Namba, K.: Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424, 643–650 (2003)

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Palo Alto Research Center, 3333 Coyote Hill Rd., Palo Alto, CA, 94304, USA

    Marshall Bern, Jindong Chen & Hao Chi Wong

  2. Departamento de Ciência da Computação, UFMG, Belo Horizonte, MG, Brazil

    Hao Chi Wong

Authors
  1. Marshall Bern
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  2. Jindong Chen
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  3. Hao Chi Wong
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Editor information

Editors and Affiliations

  1. Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Satoru Miyano

  2. Broad Institute of MIT and Harvard, 320 Charles Street, 02141-2023, Cambridge, MA, USA

    Jill Mesirov

  3. Computational Genomics Laboratory, Department of Bioengineering, Boston University, 44 Cummington St., 02215, Boston, MA, USA

    Simon Kasif

  4. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., 02912, Providence, RI, USA

    Sorin Istrail

  5. University of California, San Diego, USA

    Pavel A. Pevzner

  6. Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, 90089-2910, Los Angeles, CA, USA

    Michael Waterman

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© 2005 Springer-Verlag Berlin Heidelberg

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Bern, M., Chen, J., Wong, H.C. (2005). Avoiding Local Optima in Single Particle Reconstruction. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2005. Lecture Notes in Computer Science(), vol 3500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11415770_10

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  • DOI: https://doi.org/10.1007/11415770_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25866-7

  • Online ISBN: 978-3-540-31950-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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