Skip to main content
SpringerLink
Log in

Computational and Interpretive Genomics

  • Chapter
Biocomputing

Part of the book series: Biocomputing ((BCOM,volume 1))

Abstract

As one of its goals, this conference seeks to build bridges between two scientific cultures, represented on one side by computer scientists and physical chemists, and on the other by biologists and organic chemists. These two group are both interested in how computation can help us better understand biological systems. The motivation for joining the two cultures is heightened by the growth of genomic sequence databases, which add greatly to the amount of information describing the structure of biological macromolecules, in particular, DNA and proteins.

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 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.

References

  1. Kuhn, T. S., The Structure of Scientific Revolutions, Chicago University Press, Chicago. 1962.

    Google Scholar 

  2. Scheraga, H. A., Structural studies of ribonuclease III. A model for the secondary and tertiary structure. J. Am. Chem. Soc. 1960; 82, 3847–3852.

    Article  Google Scholar 

  3. Fasman, G. editor, Prediction of Protein Structure and the Principles of Protein Conformation, Plenum: New York, 1989.

    Google Scholar 

  4. Westheimer, F. H., Mayer, J. E., The theory of the racemization of optically active derivatives of diphenyl. J. Chem. Phys., 1946; 14, 733–738.

    Article  Google Scholar 

  5. Bush, S., Meaning of life. Electronics Weekly,07/12/00.

    Google Scholar 

  6. Echeverria, G. A., Baron, M., Punte, G., Ab initio and in-crystal geometry of trans-1,4-dibromo-1,4-dicarboxymethylcyclohexane. Structural Chem. 2000; 11, 35–40.

    Article  Google Scholar 

  7. Dunitz, J. D., Filippini, G., Gavezzotti, A.,Molecular shape and crystal packing: A study of C12H12 isomers, real and imaginary. Heiv Chim Acta 2000; 83, 2317–2335.

    Article  Google Scholar 

  8. Dunitz, J. D., Filippini, G., Gavezzotti, A., A statistical study of density and packing variations among crystalline isomers. Tetrahedron 2000; 56, 6595–6601.

    Article  Google Scholar 

  9. Lommerse, J. P. M., Motherwell, W. D. S., Ammon, H.L., et al., A test of crystal structure prediction of small organic molecules. Acta Crystallogr B 2000; 56, 697–714 Part 4.

    Article  Google Scholar 

  10. Moult, J., Hubbard, T., Fidelis, K., Pederson, J. T., Critical assessment of methods of protein structure prediction (CASP). Round III. Proteins Struct. Funct. Genet. 1999; 3, 2–6.

    Google Scholar 

  11. Hubbard, T. J. P. RMS/coverage graphs. A qualitative method for comparing three dimensional protein structure predictions. Proteins Struct. Funct. Genet. 1999; 3, 15–21.

    Google Scholar 

  12. Rossman, M. G., & Argos, P., Exploring structural homology of proteins. J. Mol. Biol. 1976; 105, 75–95.

    Article  Google Scholar 

  13. Chothia, C., Lesk, A. M., The relation between the divergence of sequence and structure in proteins. EMBO J. 1986; 5, 823–826.

    Google Scholar 

  14. Benner, S. A., Cannarozzi, G., Chelvanayagam, G. & Turcotte, M., Bona fide predictions of protein secondary structure using transparent analyses of multiple sequence alignments. Chem. Rev. 1997; 97, 2725–2843.

    Article  Google Scholar 

  15. Needleman, S. B. & Wunsch, C. D., A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 1970; 48, 443–453.

    Article  Google Scholar 

  16. Smith, T. F. & Waterman, M. S., Identification of common molecular subsequences. J. Mol. Biol. 1981; 147, 195–197.

    Article  Google Scholar 

  17. Thorne, J. L., Kishino, H. & Felsenstein, J., Inching toward reality. An improved likelihood model of sequence evolution. J. Mol. Evol. 1992; 34, 3–16.

    Article  Google Scholar 

  18. Cohen, M. A., Benner, S. A., Gonnet, G. H., Analysis of mutation during divergent evolution. The 400 by 400 dipeptide mutation matrix. Biochem. Biophys. Res. Comm. 1994; 199, 489–496.

    Article  Google Scholar 

  19. Benner, S. A., Cohen, M. A., Gonnet, G. H., Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J. Mol. Biol. 1993; 229, 1065–1082.

    Article  Google Scholar 

  20. Gonnet, G. H., Benner, S. A. Computational Biochemistry Research at ETH. Technical Report 154 Departement Informatik, 1991 Swiss Federal Institute of Technology, Zurich, Switzerland.

    Google Scholar 

  21. Gonnet, G. H., Cohen, M. A., Benner, S. A.,Exhaustive matching of the entire protein sequence database. Science 1992; 256, 1443–1445.

    Article  Google Scholar 

  22. Rost, B.; Sander, C., Prediction of protein secondary structure at better than 70-percent accuracy J. Mol. Biol. 1993; 32, 584–599.

    Article  Google Scholar 

  23. Sternberg, M. J. E., Taylor, W.R., Modeling the ATP binding site of oncogene products, the epidermal growth-factor receptor and related proteins. FEBS Lett. 1984; 175, 387–392.

    Article  Google Scholar 

  24. Benner, S. A., Gerloff, D. L., Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure. The catalytic domain of protein kinases. Adv. Enz. Regul. 1991; 31, 121–181.

    Article  Google Scholar 

  25. DeFay, T., Cohen, F. E., Evaluation of current techniques for ab initio protein structure preduction. Proteins Struct. Funct. Genet. 1995; 23, 431–445.

    Article  Google Scholar 

  26. Benner, S. A., Trabesinger-Rüf, N., Schreiber, D. R. Post-genomic science. Converting primary structure into physiological function. Adv. Enzyme Reg. 1998; 38, 155–180.

    Article  Google Scholar 

  27. Chircurel, M. Whatever happened to leptin? Nature 2000; 404, 538–540.

    Article  Google Scholar 

  28. Chandrasekharan, U. M., Sanker, S., Glynias, M. J., Karnik, S. S., Husain, A.,Angiotensin II forming activity in a reconstructed ancestral chymase. Science 1996; 271, 502–505.

    Article  Google Scholar 

  29. Liberles, D. S., Schreiber, D. R., Govindarajan, S., Chamberlin, S. G., Benner, S. A., The adaptive evolution database (TAED). Genome Biol. 2001; 2, 0003.1–0003.18

    Google Scholar 

  30. Benner, S. A., Gerloff, D. L, Chelvanayagam, G., The phospho-ßgalactosidase and synaptotagmin predictions. Proteins. Struct. Funct. Genet. 1995; 23, 446–453.

    Article  Google Scholar 

  31. Gerloff, D. L., Cohen, F. E., Korostensky, C., Turcotte, M., Gonnet, G. H., Benner, S. A., A predicted consensus structure for the N-terminal fragment of the heat shock protein HSP90 family. Proteins Struct. Funct. Genet. 1997; 27, 450–458.

    Article  Google Scholar 

  32. Tauer, A., Benner, S. A., The B 12-dependent ribonucleotide reductase from the archaebacterium Thermoplasma acidophila. An evolutionary conundrum. Proc. Natl. Acad. Sci. USA 1997; 94, 53–58.

    Article  Google Scholar 

  33. Jenny, T. F., Gerloff, D. L., Cohen, M. A., Benner, S. A., Predicted secondary and supersecondary structure for the serine/threonine specific protein phosphatase family. Proteins Struct. Funct. Genet. 1995; 21, 1–10.

    Article  Google Scholar 

  34. Benner, S. A., Trabesinger-Ruef, N., Schreiber, D. R., Post-genomic science. Converting primary structure into physiological function. Adv. Enzyme Regul. 1998; 38, 155–180.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA

    Steven A. Benner

Authors
  1. Steven A. Benner
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. University of Florida, Gainesville, Florida, USA

    Panos M. Pardalos  & Jose Principe  & 

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Kluwer Academic Publishers

About this chapter

Cite this chapter

Benner, S.A. (2002). Computational and Interpretive Genomics. In: Pardalos, P.M., Principe, J. (eds) Biocomputing. Biocomputing, vol 1. Springer, Boston, MA. https://doi.org/10.1007/978-1-4613-0259-9_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4613-0259-9_2

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-7965-2

  • Online ISBN: 978-1-4613-0259-9

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation