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J Mol Model. 2014 Jun;20(6):2278. doi: 10.1007/s00894-014-2278-5. Epub 2014 May 31.

AllerTOP v.2--a server for in silico prediction of allergens.

Author information

1
Faculty of Pharmacy, Medical University of Sofia, 2 Dunav st., 1000, Sofia, Bulgaria.

Abstract

Allergy is an overreaction by the immune system to a previously encountered, ordinarily harmless substance--typically proteins--resulting in skin rash, swelling of mucous membranes, sneezing or wheezing, or other abnormal conditions. The use of modified proteins is increasingly widespread: their presence in food, commercial products, such as washing powder, and medical therapeutics and diagnostics, makes predicting and identifying potential allergens a crucial societal issue. The prediction of allergens has been explored widely using bioinformatics, with many tools being developed in the last decade; many of these are freely available online. Here, we report a set of novel models for allergen prediction utilizing amino acid E-descriptors, auto- and cross-covariance transformation, and several machine learning methods for classification, including logistic regression (LR), decision tree (DT), naïve Bayes (NB), random forest (RF), multilayer perceptron (MLP) and k nearest neighbours (kNN). The best performing method was kNN with 85.3% accuracy at 5-fold cross-validation. The resulting model has been implemented in a revised version of the AllerTOP server (http://www.ddg-pharmfac.net/AllerTOP).

PMID:
24878803
DOI:
10.1007/s00894-014-2278-5
[Indexed for MEDLINE]

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