Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization (original) (raw)

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References

  1. Frank, J. Three-dimensional Electron Microscopy of Macromolecular Assemblies (Oxford University Press, New York, 2006).
    Book Google Scholar
  2. Orlova, E.V. & Saibil, H.R. Curr. Opin. Struct. Biol. 14, 584–590 (2004).
    Article CAS Google Scholar
  3. Heymann, J.B., Conway, J.F. & Steven, A.C. J. Struct. Biol. 147, 291–301 (2004).
    Article CAS Google Scholar
  4. Gao, H., Valle, M., Ehrenberg, M. & Frank, J. J. Struct. Biol. 147, 283–290 (2004).
    Article CAS Google Scholar
  5. Brink, J. et al. Structure 12, 185–191 (2004).
    Article CAS Google Scholar
  6. Rice, J.A. Mathematical Statistics and Data Analysis (Duxbury Press, Belmost, 1995).
    Google Scholar
  7. Sigworth, F.J. J. Struct. Biol. 122, 328–339 (1998).
    Article CAS Google Scholar
  8. Yin, Z., Zheng, Y., Doerschuk, P.C., Natarajan, P. & Johnson, J.E. J. Struct. Biol. 144, 24–50 (2003).
    Article Google Scholar
  9. Scheres, S.H.W. et al. J. Mol. Biol. 348, 139–149 (2005).
    Article CAS Google Scholar
  10. Scheres, S.H.W., Valle, M. & Carazo, J.M. Bioinformatics 21 (Suppl. 2), ii243–ii244 (2005).
    CAS PubMed Google Scholar
  11. Dempster, A.P., Laird, N.M. & Rubin, D.B. J. Royal Statist. Soc. Ser. B 39, 1–38 (1977).
    Google Scholar
  12. Valle, M. et al. EMBO J. 21, 3557–3567 (2002).
    Article CAS Google Scholar
  13. Sorzano, C.O.S. et al. J. Struct. Biol. 148, 194–204 (2004).
    Article CAS Google Scholar
  14. Gomez-Lorenzo, M.G. et al. EMBO J. 22, 6205–6213 (2003).
    Article CAS Google Scholar
  15. Valle, M. et al. Cell 114, 123–134 (2003).
    Article CAS Google Scholar

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Acknowledgements

We thank the Department of Computer Architecture and Electronics of the University of Almeria, and the Barcelona Supercomputing Center (Centro Nacional de Supercomputación) for providing computing resources, and T. Elfving for his help with weighted least-squares minimization. This work was supported by grants from the European Union (FP6-502828 and EGEE2-031688 to JMC), US National Institutes of Health (HL70472 to G.T.H. and J.M.C., and P41 RR01219 to J.F.), Howard Hughes Medical Institute (to J.F.) and the Spanish Comisión Interministerial de Ciencia y Tecnología (BFU2004-00217 to J.M.C.).

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  1. Mikel Valle
    Present address: CICBiogune, Parque Tecnológico de Bizkaia, 48160, Derio-Bizkaia, Spain

Authors and Affiliations

  1. Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, 28049, Spain
    Sjors H W Scheres, Mikel Valle & Jose-Maria Carazo
  2. Howard Hughes Medical Institute, Health Research Inc., Empire State Plaza, Albany, 12201, New York, USA
    Haixiao Gao & Joachim Frank
  3. The Graduate Center, City University of New York, New York, 10016, New York, USA
    Gabor T Herman
  4. Food and Resource Economics, University of Delaware, Newark, 19716, Delaware, USA
    Paul P B Eggermont

Authors

  1. Sjors H W Scheres
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  2. Haixiao Gao
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  3. Mikel Valle
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  4. Gabor T Herman
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  5. Paul P B Eggermont
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  6. Joachim Frank
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  7. Jose-Maria Carazo
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Correspondence toJose-Maria Carazo.

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The authors declare no competing financial interests.

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Scheres, S., Gao, H., Valle, M. et al. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.Nat Methods 4, 27–29 (2007). https://doi.org/10.1038/nmeth992

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