Correlation between the location of antigenic sites and the prediction of turns in proteins

Immunol Lett. 1993 Apr;36(1):83-99. doi: 10.1016/0165-2478(93)90072-a.

Abstract

In the present study, we developed new turn scales based on the occurrence of amino acids at each of the four positions of a turn using a structural database comprised of 87 proteins. We found that the scales correctly predicted a fraction of the turn regions in proteins with approximately 80% confidence. We used the turn scales for predicting the location of antigenic sites in proteins. The method was developed with the specific aim of predicting only a few peaks for each protein (two or three). We found that it leads to a high level of accurate prediction (70% of correct prediction of known epitopes). Our method should be useful for selecting protein regions to be synthesized in order to produce anti-peptide antibodies cross-reacting with the parent protein.

MeSH terms

  • Amino Acid Sequence
  • Databases, Factual
  • Epitopes / chemistry*
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Secondary*
  • Proteins / chemistry*

Substances

  • Epitopes
  • Proteins