Skip to main content
SpringerLink
Log in

Characterization of Protein Structure and Function at Genome Scale with a Computational Prediction Pipeline

  • Chapter
Genetic Engineering

Part of the book series: Genetic Engineering: Principles and Methods ((GEPM,volume 25))

Abstract

Recent advances in high-throughput production capabilities for biological data such as genomic sequence (1,2), large-scale gene expression data (3-5), genomescale protein-protein interactions (6,7), and protein structures (8), arc revolutionizing the biological sciences. Essential to this new revolution are capabilities to computationally interpret large quantities of biological data generated under various experimental conditions and build mathematical models that fit these data. The combination of on-line bioinformatics tools and easy access to the high-speed Internet has made it generally possible to facilitate such computational steps and make biological discoveriesin silicoin a highly efficient manner. By utilizing various bioinformatics prediction, analysis and modeling tools, one can quickly generate hypotheses and theoretical models, which could then guide the design of experiments for further validation. The paradigm that links and integrates systematic data generation, computational data interpretation, and experimental validation is clearly providing a new and powerful way for conducting biological research. The focus of this paper is on (a) development of new computational tools for interpretation of large quantity of genomic sequence data for structural and functional inference and (b) example applications of these tools to studies of microbial genomes, particularlycyanobacterialgenomes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Lander, E.C. et al. (2001) Nature 409, 860–921.

    Article  PubMed  CAS  Google Scholar 

  2. Venter, V.C. et al. (2001) Science 291, 1304–1351.

    Article  PubMed  CAS  Google Scholar 

  3. DeRisi, J.L., Iyer, V.R. and Brown, P.O. (1997) Science 278, 680–686.

    Article  PubMed  CAS  Google Scholar 

  4. Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O. and Hershkowitz, I. (1998) Science 282, 699–705.

    Article  PubMed  CAS  Google Scholar 

  5. Zhu, G., Spellman, P.T., Volpe, T., Brown, P.O., Botstein, D., Davis, T.N. and Futcher, B. (2000) Nature 406, 90–94.

    Article  PubMed  CAS  Google Scholar 

  6. Fields, S. and Song, O. (1989) Nature 340, 245–246.

    Article  PubMed  CAS  Google Scholar 

  7. Ho, Y. et al. (2002) Nature 415, 180–183.

    Article  PubMed  CAS  Google Scholar 

  8. Chance, M.R., Bresnick, A.R., Burley, S.K., Jiang, J.S., Lima, C.D., Sali, A., Almo, S.C., Bonanno, J.B., Buglino, J.A., Boulton, S., Chen, H., Eswar, N., He, G., Huang, R., Ilyin, V., McMahan, L., Pieper, U., Ray, S., Vidal, M. and Wang, L.K. (2002) Protein Sci. 11, 723–738.

    Article  PubMed  CAS  Google Scholar 

  9. Altschul, S.F., Madden T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Nucl. Acids Res. 25, 3389–3402.

    Article  PubMed  CAS  Google Scholar 

  10. CASP (1995) Proteins: Struct. Funct. Genet. 23, 295–462.

    Google Scholar 

  11. CASP (1997) Proteins: Struct. Funct. Genet., Suppl. 1 29, 1–230.

    Google Scholar 

  12. CASP (1999) Proteins: Struuct. Funct. Genet. Suppl. 3 37, 1–237.

    Google Scholar 

  13. CASP (2001) Proteins: Struct. Funct. Genet. Suppl. 4 45, 1–199.

    Google Scholar 

  14. CASP (2002) CASPS Proceedings.

    Google Scholar 

  15. Xu, D., Baburaj, K., Peterson, C.B. and Xu, Y. (2001b) Proteins: Struct. Funct. Genet. 44, 312–320.

    CAS  Google Scholar 

  16. Sali, A. and Blundell, T.L. (1993) J. Mol. Biol. 234, 779–815.

    Article  PubMed  CAS  Google Scholar 

  17. Bowie, J.U., Luthy, R. and Eisenberg, D. (1991) Science 253, 164–170.

    Article  PubMed  CAS  Google Scholar 

  18. Li, Z. and Scheraga, H.A. (1987) Proc. Nat. Acad. Sci. U.S.A. 84, 6611–6615.

    Article  CAS  Google Scholar 

  19. Skolnick, J. and Kolinski, A. (1991) J. Mol. Biol. 221, 499–531.

    Article  PubMed  CAS  Google Scholar 

  20. Westbrook, J., Feng, Z., Jain, S., Bhat, T.N., Thanki, N., Ravichandran, V., Gilliland, G.L., Bluhm, W., Weissig, H., Greer, D.S., Bourne, P.E. and Berman, H.M. (2002) Nucl. Acids Res. 30, 245–248.

    Article  PubMed  CAS  Google Scholar 

  21. Montelione, G.T. and Anderson, S. (1999) Nature Struct. Biol. 6, 11–12.

    Article  PubMed  CAS  Google Scholar 

  22. Karplus, K., Barrett, C. and Hughey, R. (1998) Bioinformatics 14, 846–856.

    Article  PubMed  CAS  Google Scholar 

  23. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) Nature 358, 86–89.

    Article  PubMed  CAS  Google Scholar 

  24. Xu, Y. and Xu, D. (2000) Protein: Struct. Funct. Genet. 40, 343–354.

    CAS  Google Scholar 

  25. Wetlaufer, D.B. (1978) Proc. Nat. Acad. Sci. U.S.A. 70, 697–701.

    Article  Google Scholar 

  26. Xu, Y., Xu, D., Crawford, O.H., Einstein, J.R., Larimer, F., Uberbacher, E.C., Unseren, M.A. and Zhang, G. (1999) Protein Engin. 12, 899–907.

    CAS  Google Scholar 

  27. Xu, D., Crawford, O.H., LoCascio, P.F. and Xu, Y. (2001a) Proteins: Struct. Funct. Genet. (CASP4 Special Issue) 46, 140–148.

    Google Scholar 

  28. Xu, D. and Xu, Y. (2002) In Protein Structure Prediction: Bioinformatic Approach (Igor Tsigelny, ed.) International University Line publishers (IUL), LaJolla, CA. pp. 5–41.

    Google Scholar 

  29. Nielsen, H., Engelbrecht, J., Brunak, S. and von Heijne, G. (1997) Protein Engin. 10, 1–6.

    CAS  Google Scholar 

  30. Corpet, F., Servant, F., Gouzy, J. and Kahn, D. (2000) Nucl. Acids Res. 28, 267–269.

    Article  PubMed  CAS  Google Scholar 

  31. Jones, D.T. (1999) J. Mol. Biol. 287, 797–815.

    Article  PubMed  CAS  Google Scholar 

  32. Bairoch, A. and Apweiler, R. (1999) Nucl. Acids Res. 27, 49–54.

    Article  PubMed  CAS  Google Scholar 

  33. Hirokawa, T., Boon-Cheing, S. and Mitaku, S. (1998) Bioinformatics 14, 378–379.

    Article  PubMed  CAS  Google Scholar 

  34. Miyazawa, S. and Jernigan, R.L. (1996) J. Mol. Biol. 256, 623–644.

    Article  PubMed  CAS  Google Scholar 

  35. Kim, D., Xu, D., Guo, J., Ellrott, K. and Xu, Y. (2002) (submitted).

    Google Scholar 

  36. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) J. Mol. Biol. 247, 536–540.

    PubMed  CAS  Google Scholar 

  37. Xiang, Z. and Honig, B. (2001) J. Mol. Biol. 311, 421–430.

    Article  PubMed  CAS  Google Scholar 

  38. Vriend, G. (1990) J. Mol. Graphics 8, 52–56.

    Article  CAS  Google Scholar 

  39. Hofmann, K., Bucher, P., Falquet, L. and Bairoch, A. (1999) Nucl. Acids Res. 27, 215–219.

    Article  PubMed  CAS  Google Scholar 

  40. Attwood, T.K., Flower D.R., Lewis, A.P., Mabey, J.E., Morgan, S.R., Scordis, P., Selley, J. and Wright, W. (1999) Nucl. Acids Res. 27, 220–225.

    Article  PubMed  CAS  Google Scholar 

  41. Henikoff, J.G., Henikoff, S. and Pietrokovski, S. (1999) Nucl. Acids Res. 27, 226–228.

    Article  PubMed  CAS  Google Scholar 

  42. Burley, S.K., Almo, S.C., Bonanno, J.B., Capel, M., Chance, M.R. Gaasterland, T., Lin, D., Sali, A., Studier, F.W. and Swaminathan, S. (1999) Nature Genet. 23, 151–157.

    Article  PubMed  CAS  Google Scholar 

  43. Vakser, I.A. (1996) Biopolymers 39, 455–464.

    Article  PubMed  CAS  Google Scholar 

  44. Zhang, B., Rychlewski, L., Pawlowski, K., Fetrow, J.S., Skolnick, J. and Godzik, A. (1999) Protein Sci. 8, 1104–1115.

    Article  PubMed  CAS  Google Scholar 

  45. Wallace, A.C., Laskowski, R.A. and Thornton, J.M. (1996) Protein Sci. 5, 1001–1013.

    Article  PubMed  CAS  Google Scholar 

  46. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M. and Sonnhammer, E.L.L. (2002) Nucl. Acids Res. 30, 276–280.

    Article  PubMed  CAS  Google Scholar 

  47. Nakai, K. and Horton, P. (1999) Trends in Biochem. Sci. 24, 34–35.

    CAS  Google Scholar 

  48. Honig, B. and Nicholls, A. (1995) Science 268,1144–1149.

    Article  PubMed  CAS  Google Scholar 

  49. Nicholls, A., Sharp, K.A. and Honig, B. (1991) Proteins: Struct. Funct. Genet. 11, 281–296.

    CAS  Google Scholar 

  50. Chisholm, S.W. (1992) in Primary Productivity and Biogeochemical Cycles. (Falkowski P.G. and Woodhead, A.D., eds.) Plenum Press, NY pp. 213–237.

    Google Scholar 

  51. Partensky, F., Hess, W.R. and Vaulot, D. (1999) Microbiol. Mol. Biol. Rev. 63, 106–127.

    CAS  Google Scholar 

  52. Qian, J., Dolled-Filhart, M., Lin, J., Yu, H. and Gerstein, M. (2001) J. Mol. Biol. 314, 1053–1066.

    Article  PubMed  CAS  Google Scholar 

  53. Cannon, G.C., Bradburne, C.E., Aldrich, H.C., Baker, S.H., Heinhorst, S. and Shively, J.M. (2001) Appl. Env. Microbiol. 67, 5351–5361.

    Article  CAS  Google Scholar 

  54. Friedberg, D., Jager, K.M., Kessel, M., Silman, N.J. and Bergman, B. (1993) Mol. Microbiol. 9, 1193–1201.

    Article  PubMed  CAS  Google Scholar 

  55. English, R.S., Lorbach, S.C., Qin, X. and Shively, J.M. (1994) Mol. Microbiol. 12, 647–654.

    Article  PubMed  CAS  Google Scholar 

  56. Baker, S.H., Lorbach, S.C., Rodriguez-Buey, M., Buey, M., Williams, D.S., Aldrich, H. and Shively, J.M. (1999) Arch. Microbiol. 172(4) 233–239.

    Article  PubMed  CAS  Google Scholar 

  57. Baker, S.H., Williams, D.S., Aldrich, H.C., Gambrell, A.C. and Shively, J.M. (2000) Arch. Microbiol. 173, 278–283.

    Article  PubMed  CAS  Google Scholar 

  58. Price, G.D., Howitt, S.M., Harrison, K. and Badger, M.R. (1993) J. Bacteriol. 175, 2871–2879.

    PubMed  CAS  Google Scholar 

  59. Shively, J.M., Lorbach, S.C., Jin, S. and Baker, S.H. (1996) in Microbial Growth on Cl Coupounds (Lidstrom, M. and Tabita, F.R., eds.) Kluwer Academic Publishers B.V., Dordrecht, The Netherlands. pp. 56–63.

    Google Scholar 

  60. Tabita, F.R., Gibson, J.L., Falcone, D.L., Lee, B.G. and Chen, J.H. (1990) FEMS Microbiol. Rev. 7, 437–443.

    PubMed  CAS  Google Scholar 

  61. Orus, M.I., Rodriguez, M.L., Martinez, F. and Marco, E. (1995) Plant Physiol. 107, 1159–1166.

    PubMed  CAS  Google Scholar 

  62. Kovacs, E., van der Vies, S.M., Glatz, A., Torok, Z., Varvasovszki, V., Horvath, I. and Vigh, L. (2001) Biochem. Biophys. Res. Commun. 289, 908–915.

    CAS  Google Scholar 

  63. Leahy, D.J., Erickson, H.P., Aukhil, I., et al. (1994) Proteins 19(1), 48–54.

    Article  PubMed  CAS  Google Scholar 

  64. Steward, A., Adhya, S. and Clarke, J. (2002) J. Mol. Biol. 318, 935–940.

    Article  PubMed  CAS  Google Scholar 

  65. Shah, M., Passovets, S., Kim, D., Ellrott, K., Wang, L., Vokler, I., LoCascio, P., Xu, D. and Xu, Y. (2003) in Proceeding of the 3rdIEEE Symposium on Bioinformatics and Bioengineering. In press.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA

    Dong Xu, Dongsup Kim, Phuongan Dam, Manesh Shah, Edward C. Uberbacher & Ying Xu

  2. Computer Sciences and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA

    Ying Xu

  3. Protein Informatics Group, Oak Ridge National Laboratory, 1060 Commerce Park Drive, Oak Ridge, 37831-6480, TN, USA

    Dong Xu

Authors
  1. Dong Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dongsup Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Phuongan Dam
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Manesh Shah
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Edward C. Uberbacher
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ying Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Brookhaven National Laboratory, Upton, New York, USA

    Jane K. Setlow

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer Science+Business Media New York

About this chapter

Cite this chapter

Xu, D., Kim, D., Dam, P., Shah, M., Uberbacher, E.C., Xu, Y. (2003). Characterization of Protein Structure and Function at Genome Scale with a Computational Prediction Pipeline. In: Setlow, J.K. (eds) Genetic Engineering. Genetic Engineering: Principles and Methods, vol 25. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-0073-5_12

Download citation

  • DOI: https://doi.org/10.1007/978-1-4615-0073-5_12

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-4911-2

  • Online ISBN: 978-1-4615-0073-5

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation