Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties

Irini A. Doytchinova, Darren R. Flower

Research output: Contribution to journalArticle

Abstract

Subunit vaccine discovery is an accepted clinical priority. The empirical approach is time- and labor-consuming and can often end in failure. Rational information-driven approaches can overcome these limitations in a fast and efficient manner. However, informatics solutions require reliable algorithms for antigen identification. All known algorithms use sequence similarity to identify antigens. However, antigenicity may be encoded subtly in a sequence and may not be directly identifiable by sequence alignment. We propose a new alignment-independent method for antigen recognition based on the principal chemical properties of protein amino acid sequences. The method is tested by cross-validation on a training set of bacterial antigens and external validation on a test set of known antigens. The prediction accuracy is 83% for the cross-validation and 80% for the external test set. Our approach is accurate and robust, and provides a potent tool for the in silico discovery of medically relevant subunit vaccines.
Original languageEnglish
Pages (from-to)856-866
Number of pages11
JournalVaccine
Volume25
Issue number5
Early online date28 Sep 2006
DOIs
Publication statusPublished - 15 Jan 2007

Keywords

  • vaccine
  • antigen prediction

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