AllerTOP v. 2.0
Bioinformatics tool for allergenicity prediction
The method is based on auto cross covariance (ACC) transformation of protein sequences into uniform equal-length vectors. ACC is a protein sequence mining method developed by Wold et al. (Anal. Chim. Acta 1993;277:239-253). It has been applied to quantitative structure-activity relationships (QSAR) studies of peptides with different length.
The principal properties of the amino acids were represented by five E descriptors, originally derived by Venkatarajan and Braun (J. Mol. Model (2001) 7:445–453). They describe amino acid hydrophobicity, molecular size, helix-forming propensity, relative abundance of amino acids, and β-strand forming propensity.
The proteins are classified by k-nearest neighbor algorithm (kNN,k=1) based on training set containing 2427 known allergens from different species and 2427 non-allergens.