Amino Acids

, Volume 33, Issue 3, pp 423–428 | Cite as

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

  • J. Chen
  • H. Liu
  • J. Yang
  • K.-C. Chou


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.

Keywords: B-cell epitope – AAP antigenicity scale – SVM classifier 



amino acid pair


support vector machine


receiver operating characteristics


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Supplementary material

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • J. Chen
    • 1
  • H. Liu
    • 1
  • J. Yang
    • 1
  • K.-C. Chou
    • 1
    • 2
  1. 1.Institute of Image Processing and Pattern RecognitionShanghai Jiaotong UniversityShanghaiChina
  2. 2.Gordon Life Science InstituteSan DiegoU.S.A.

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