Prediction of linear B-cell epitopes using amino acid pair antigenicity scale

Jun Chen, H. Liu, J. Yang, K. C. Chou

Research output: Contribution to journalArticle

335 Citations (Scopus)

Abstract

Identification of antigenic sites on proteins is of vital importance for developing synthetic peptide vaccines, immunodiagnostic tests and antibody production. Currently, most of the prediction algorithms rely on amino acid propensity scales using a sliding window approach. These methods are oversimplified and yield poor predicted results in practice. In this paper, a novel scale, called the amino acid pair (AAP) antigenicity scale, is proposed that is based on the finding that B-cell epitopes favor particular AAPs. It is demonstrated that, using SVM (support vector machine) classifier, the AAP antigenicity scale approach has much better performance than the existing scales based on the single amino acid propensity. The AAP antigenicity scale can reflect some special sequence-coupled feature in the B-cell epitopes, which is the essence why the new approach is superior to the existing ones. It is anticipated that with the continuous increase of the known epitope data, the power of the AAP antigenicity scale approach will be further enhanced.

Original languageEnglish (US)
Pages (from-to)423-428
Number of pages6
JournalAmino Acids
Volume33
Issue number3
DOIs
StatePublished - Sep 2007
Externally publishedYes

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B-Lymphocyte Epitopes
Amino Acids
Synthetic Vaccines
Subunit Vaccines
Antibody Formation
Support vector machines
Epitopes
Classifiers
Antibodies
Proteins

Keywords

  • AAP antigenicity scale
  • B-cell epitope
  • SVM classifier

ASJC Scopus subject areas

  • Biochemistry
  • Clinical Biochemistry
  • Organic Chemistry

Cite this

Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. / Chen, Jun; Liu, H.; Yang, J.; Chou, K. C.

In: Amino Acids, Vol. 33, No. 3, 09.2007, p. 423-428.

Research output: Contribution to journalArticle

Chen, Jun ; Liu, H. ; Yang, J. ; Chou, K. C. / Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. In: Amino Acids. 2007 ; Vol. 33, No. 3. pp. 423-428.
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