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

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 oversim...

Full description

Saved in:
Bibliographic Details
Published in:Amino acids 2007-09, Vol.33 (3), p.423-428
Main Authors: Chen, J, Liu, H, Yang, J, Chou, K.-C
Format: Article
Language:English
Subjects:
AAP antigenicity scale
Algorithms
Amino Acid Sequence
Amino acids
Amino Acids - genetics
Amino Acids - immunology
Antibodies
B-cell epitope
Classifiers
Epitopes, B-Lymphocyte - genetics
Epitopes, B-Lymphocyte - immunology
Molecular Sequence Data
Pattern Recognition, Automated
Proteins
Proteins - genetics
Proteins - immunology
Random Allocation
Reproducibility of Results
Sensitivity and Specificity
Sliding
Support vector machines
SVM classifier
Vaccines
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0939-4451
1438-2199
DOI:10.1007/s00726-006-0485-9