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Genomics and Proteomics pp 179–189Cite as

Linking Structural Biology With Genome Research

The Berlin “Protein Structure Factory” Initiative

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References

  1. McKusick, V.A. (1997) Genomics: Structural and functional studies of genomes. Genomics 45, 244–249.

    PubMed  CAS  Google Scholar 

  2. Šali, A. (1998) 100,000 protein structures for the biologist. Nature Struct. Biol. 5, 1029–1032.

    PubMed  Google Scholar 

  3. Tenwilliger, T.C., Waldo, G., Peat, T.S., Newman, J.M., Chu, K., and Berendzen, J. (1998) Class-directed structure determination: Foundation for a protein structure initiative. Protein Sci. 7, 1851–1856.

    Google Scholar 

  4. Shapiro, L. and Lima, C.D. (1998) The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science. Structure 6, 265–267.

    Article  PubMed  CAS  Google Scholar 

  5. Gaasterland, T. (1998) Structural genomics taking shape. Trends Genet. 14, 135.

    Article  PubMed  CAS  Google Scholar 

  6. Koonin, E.V., Tatusov, R.L., and Galperin, M.Y. (1998) Beyond complete genomes: from sequence to structure and function. Current Opinion Struct. Biol. 8, 355–363.

    CAS  Google Scholar 

  7. Finkelstein, A.V. and Ptitsyn, O.B. (1987) Why do all globular proteins fit the limited set of folding patterns? Prog. Biophys. Mol. Biol. 50, 171–190.

    PubMed  CAS  Google Scholar 

  8. Chothia, C.(1992) One thousand protein families for the molecular biologist. Nature 357, 543–544.

    Article  PubMed  CAS  Google Scholar 

  9. Orengo, C.A., Jones, D.T., and Thornton, J.M. (1994) Protein superfamilies and domain superfolds. Nature 372, 631–634.

    Article  PubMed  CAS  Google Scholar 

  10. Bork, P. and Eisenberg, D. (1998) Sequences and topology. Deriving biological knowledge from genomic sequences. Current Opinion Struct. Biol. 8, 331–332.

    CAS  Google Scholar 

  11. Fischer, D. and Eisenberg, D. (1996) Protein fold recognition using sequence-derived predictions. Protein Sci. 5, 947–955.

    PubMed  CAS  Google Scholar 

  12. Rice, D.W. and Eisenberg, D. (1997) A 3D-ID substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J. Mol. Biol. 267, 1026–1038.

    Article  PubMed  CAS  Google Scholar 

  13. Fischer, D. and Eisenberg, D. (1997) Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc. Natl. Acad. Sci. USA 94, 11929–11934.

    Article  PubMed  CAS  Google Scholar 

  14. Huynen, M., Doerks, T., Eisenhaber, E, Orengo, C., Sunyaev, S., Yuan, Y., and Bork, P. (1998) Homology-based fold predictions for Mycoplasma genitalium proteins. J. Mol. Biol. 280, 323–326.

    Article  PubMed  CAS  Google Scholar 

  15. Kim, K.K., Hung, L.-W., Yokota, H., Kim, R., and Kim, S.-H. (1998) Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 Å resolution. Proc. Natl. Acad. Sci. USA 95, 10419–10424.

    PubMed  CAS  Google Scholar 

  16. Lim, J.-H., Yu, Y.G., Han, YS., Cho, S.-j., Ahn, B.-Y, Kim, S.-H., and Cho, Y. (1997) Thecrystal structure of an Fe-superoxide dismutase from the hyperthermophile Aquifex pyrophilus at 1.9 Å resolution: Structural basis for thermostability. J. Mol. Biol. 270, 259–274.

    Article  PubMed  CAS  Google Scholar 

  17. Kim, K.K., Kim, R., and Kim, S.-H. (1998) Crystal structure of a small heat-shock protein. Nature 394, 595–599.

    Article  PubMed  CAS  Google Scholar 

  18. Saegusa, A. (1998) Japan’s genome programme goes ahead, with protein analysis. Nature 392, 219.

    PubMed  CAS  Google Scholar 

  19. Kim, S.-H. (1998) Shining light on structural genomics. Nature Struct. Biol. 5, 643–445.

    Article  PubMed  CAS  Google Scholar 

  20. Bork, P.and Koonin, E.V. (1998) Predicting functions from protein sequences-where are the bottlenecks? Nature Genetics 18, 313–318.

    Article  PubMed  CAS  Google Scholar 

  21. Schultz, J., Milpetz, F., Bork, P., and Ponting, C.P. (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl. Acad. Sci. USA 95, 5857–5864.

    PubMed  CAS  Google Scholar 

  22. Bork, P., Dandekar, T., Eisenhaber, F., and Huynen, M. (1998) Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases. J. Mol. Med. 76, 77–79.

    Article  PubMed  CAS  Google Scholar 

  23. Yuan, Y., Schultz, J., Mlodzik, M., and Bork, P. (1997) Secreted Fringe-like signaling molecules may be glycosyltransferases. Cell 88, 9–1 I.

    Article  PubMed  CAS  Google Scholar 

  24. Museghian, A.R., Bassett, D.E., Jr., Boguski, M., Bork, P., and Koonin, E.V. (1997) Positionally cloned human disease genes: New motifs and evolutionary conservation. Proc. Natl. Acad. Sci. USA 94, 5831–5836.

    Google Scholar 

  25. Bork, P., Hofmann, K., Bucher, P., Neuwald, A., Altschul, S.F., and Koonin, E.V. (1997) A superfamily of conserved domains in DNA damage-reponsive cell cycle checkpoint proteins. FASEB J. 11, 68–76.

    PubMed  CAS  Google Scholar 

  26. Maier, E., Maier-Ewert, S., Bancroft, D., and Lehrach, H. (1997) Automated array technologies for gene expression profiling. Drug Discovery Today 2, 315–324.

    Article  Google Scholar 

  27. Maier, E., Maier-Ewert, S., Ahmadi, R., Curtis, J., and Lehrach, H. (1994) Application of robotic technology to automated sequence fingerprint analysis by oligonucleotide hybridisation. J. Biotech. 35, 191–203.

    Article  CAS  Google Scholar 

  28. Hochuli, E., Bannwarth, W., Dobeli, H., Gentz, R., and Stüber, D. (1988) Genetic approach to facilitate purification of recombinant proteins with a novel metal chelate adsorbent. Bio/Technology 6, 1321–1325.

    Article  CAS  Google Scholar 

  29. Schmidt, T.G.M. and Skerra, A. (1994). One-step affinity purification of bacterially produced proteins by means of the “Strep-tag” and immobilized recombinant core streptavidin. J. Chromatogr. A 676, 337–345.

    Article  PubMed  CAS  Google Scholar 

  30. Oschkinat, H. and Croft, D. (1994). Automated assignment of multidimensional nuclear magnetic resonance spectra. H. Meth. Enzymol. 239, 308–318.

    CAS  Google Scholar 

  31. Nilges, M., Macias, M.C., O’Donoghue, S.I., and Oschkinat, H. (1997). Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin. J. Mol. Biol. 269, 408–422.

    Article  PubMed  CAS  Google Scholar 

  32. Weber, P.C. (1997) Overview of protein crystallization methods. Methods Enzymol. 276, 13–22.

    CAS  Google Scholar 

  33. Earnest, T. (1995) Conceptual Design Report for ALS Beamline 5.0, Lawrence Berkeley Laboratory PN941209-2.

    Google Scholar 

  34. Svensson, L.A., Ståhl, K., Cerenius, Y., Oskarsson, Å., Albertsson, J., and Liljas, A. (1997) A new beamline for crystallographic measurements at the MAX II synchrotron, Lund, Sweden, Annual Repor 182.

    Google Scholar 

  35. Ogata, C.M. (1998) MAD phasing grows up. Nature Struct. Biol. 5, 638–640.

    Article  PubMed  CAS  Google Scholar 

  36. Hendrickson, W.A. and Ogata, C.M. (1997) Phase determination from multiwavelength anomalous diffraction measurements. Methods Enzymol. 276, 494–523.

    CAS  Google Scholar 

  37. Muller, A., Muller, J.J., Muller, Y.A., Uhlmann, H., Bernhardt, R., and Heinemann, U. (1998) New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4-108). Structure 6, 269–280.

    PubMed  CAS  Google Scholar 

  38. Fortier, S., Chiverton, A., Glasgow, J., and Leherte, L. (1997) Critical-point analysis in protein electrondensity map interpretation. Methods Enzymol. 277, 131–157.

    PubMed  CAS  Google Scholar 

  39. Lamzin, V.S. and Wilson, K.S. (1997) Automated refinement for protein crystallography. Methods Enzymol. 277, 269–305.

    CAS  Google Scholar 

  40. Dodson, E.J., Davies, G.J., Lamzin, V.S., Murshudov, G.N., and Wilson, K.S. (1998) Validation tools: can they indicate the information content of macromolecular crystal structures? Structure 6, 685–690.

    Article  PubMed  CAS  Google Scholar 

  41. Brownstein, M.J., Trent, J.M., and Boguski, M.S. (1998) Functional genomics. Trends Biochem. Sci. 23(Suppl.), 27–29.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Forschungsgruppe Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Berlin

    Udo Heinemann

  2. Institut für Kristallographie, Freie Universitôt Berlin, Berlin, Germany

    Udo Heinemann, Gerd Illing, Hartmut Oschkinat & Wolfram Saenger

  3. BioteCon, Gesellschaft für Biotechnologie und Consulting mbH, Potsdam

    Juergen Frevert

  4. Institut für Medizinische Physik und Biophysik, Klinikum Charité der Humboldt-Universität zu, Berlin, Germany

    Klaus-Peter Hofman

  5. Interdisziplinärer Forschungsverbund Strukturbiologie, Berlin

    Gerd Illing

  6. Forschungsinstitut für Molekulare Pharmakologie, Berlin

    Hartmut Oschkinat

  7. Max-Planck-Gesellschaft zur Förderung der Wissenschaften, Ressourcenzentrum im DHGP am MPI für molekulare Genetik, Berlin

    Rolf Zettl

Authors
  1. Udo Heinemann
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  2. Juergen Frevert
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  3. Klaus-Peter Hofman
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  4. Gerd Illing
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  5. Hartmut Oschkinat
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  6. Wolfram Saenger
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  7. Rolf Zettl
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Editor information

Editors and Affiliations

  1. Deutsches Krebsforschungszentrum, Heidelberg, Germany

    Sándor Suhai

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© 2002 Kluwer Academic Publishers

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Heinemann, U. et al. (2002). Linking Structural Biology With Genome Research. In: Suhai, S. (eds) Genomics and Proteomics. Springer, Boston, MA. https://doi.org/10.1007/0-306-46823-9_15

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  • DOI: https://doi.org/10.1007/0-306-46823-9_15

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-0-306-46312-9

  • Online ISBN: 978-0-306-46823-0

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