Problems and Progress in Computational Approaches to the Molecular Basis of Recognition

  • Charles DeLisi
  • Ugur Sezerman
  • Rakefet Rosenfeld
Conference paper
Part of the The Jerusalem Symposia on Quantum Chemistry and Biochemistry book series (JSQC, volume 25)


Computational methods for identifying functional properties of proteins are briefly discussed. The methods lead to the concept of structure-function motif. A specific example is alpha amphipathicity as an indicator of antigenicity. This motif, though useful for planning experiments, is not sufficiently reliable to provide the basis for vaccine design. Recent progress on docking strategies based on structural analyses may provide methods that will be useful for both protein and nucleic acid receptors.


Antigenic Site Phospho Choline Protein Structure Determination Serine Proteinase Domain Amino Acid Variability 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. [1]
    DeLisi, C. (1988) Computers in molecular biology: current applications and emerging trends. Science, 240:47–52.PubMedCrossRefGoogle Scholar
  2. [2]
    Benham, C. J. (1986) Superhelical DNA, Comments Mol. Cell Biophys. 4: 35–54.Google Scholar
  3. [3]
    C. Branden and J. Tooze (1991), Introduction to Protein Structure, Garland Publishing Inc., New York.Google Scholar
  4. [4]
    Gilbert W. (1978) Why genes in pieces? Nature 271:501PubMedCrossRefGoogle Scholar
  5. [5]
    Klein, P., J. Jacquez, and C. DeLisi (1986) Prediction of protein function by discriminant analysis, Math Biosci,81: 177–189.CrossRefGoogle Scholar
  6. [6a]
    Bairoch, A. (1991) PROSITE: A dictionary of sites and petterns in proteins. Nucl. Acids Res., 19:2241–2245.PubMedCrossRefGoogle Scholar
  7. [6b]
    Henikoff, S., Henikoff, J.G. (1991) Automated assembly of protein blocks for database searching. Nucl. Acids Res., 19:6565–6572.PubMedCrossRefGoogle Scholar
  8. [7]
    Rosenfeld, R., M. Colbert, N. Soohoo and C. DeLisi, in preparation.Google Scholar
  9. [8]
    Wu T.T. and E. A. Kabat (1970) An analysis of the sequence of bence Joners protein and myeloma light chains and their implication for antibody complementarity. J. Exp. Med. 132, 211–250PubMedCrossRefGoogle Scholar
  10. [9]
    DeLisi, C., and J. Berzofsky (1985) T-cell antigenic sites are amphipathic structures, Proc. Nat. Acad. Sci. USA, 82: 7048–7052.CrossRefGoogle Scholar
  11. [10]
    DeLisi, C., J. Cornette, H. Margalit, K. Cease, and J. A. Berzofsky (1987) The role of amphipathicity as an indicator of T-cell antigenic sites on proteins Ili. Immunogenicity of Protein Antigens: Repertoire and Regulation. Sercarz, E.G., and Berzofsky, J.A. (Eds) CRC Press, Boca Raton. Vol 1, 35–42Google Scholar
  12. [11]
    Berzofsky, J., A. Bensassan, K. B. Cease et al (1988) Antigenic peptides recognized by T-lymphocytes from AIDS viral envelope immune humans. Nature 334:706.PubMedCrossRefGoogle Scholar
  13. [12]
    Klein, P., M. Kanehisa and C. DeLisi (1985) The detection and classification of membrane spanning proteins, Biochemica et Biophysica Acta, 815, 468.CrossRefGoogle Scholar
  14. [13]
    Vajda, S. and C. DeLisi (1990) Fast prediction of the backbone structure in low energy polypeptide conformations by discrete dynamic programming, Biopolymers, 29:1755–1772.PubMedCrossRefGoogle Scholar
  15. [14]
    Sezerman, O. S., S. Vajda, and C. DeLisi. Docking of flexible peptides to compliant receptors with applications to ligand-MHC interactions, SubmittedGoogle Scholar
  16. [15]
    Brower R. C. and C. DeLisi Impact of massively parallel computation on protein structure determination, SubmittedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 1992

Authors and Affiliations

  • Charles DeLisi
    • 1
  • Ugur Sezerman
    • 1
  • Rakefet Rosenfeld
    • 1
  1. 1.Department of Biomedical EngineeringBoston University College of EngineeringBostonUSA

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