AllerCatPro - Prediction of protein allergenicity potential from the protein sequence

AllerCatPro - Prediction of protein allergenicity potential from the protein sequence
Title:
AllerCatPro - Prediction of protein allergenicity potential from the protein sequence
Other Titles:
Bioinformatics
DOI:
10.1093/bioinformatics/btz029
Keywords:
Publication Date:
18 January 2019
Citation:
Sebastian Maurer-Stroh, Nora L Krutz, Petra S Kern, Vithiagaran Gunalan, Minh N Nguyen, Vachiranee Limviphuvadh, Frank Eisenhaber, G Frank Gerberick, AllerCatPro—prediction of protein allergenicity potential from the protein sequence, Bioinformatics, Volume 35, Issue 17, 1 September 2019, Pages 3020–3027, https://doi.org/10.1093/bioinformatics/btz029
Abstract:
MOTIVATION: Due to the risk of inducing an immediate Type I (IgE-mediated) allergic response, proteins intended for use in consumer products must be investigated for their allergenic potential before introduction into the marketplace. The FAO/WHO guidelines for computational assessment of allergenic potential of proteins based on short peptide hits and linear sequence window identity thresholds misclassify many proteins as allergens. RESULTS: We developed AllerCatPro which predicts the allergenic potential of proteins based on similarity of their 3D protein structure as well as their amino acid sequence compared with a data set of known protein allergens comprising of 4180 unique allergenic protein sequences derived from the union of the major databases Food Allergy Research and Resource Program, Comprehensive Protein Allergen Resource, WHO/International Union of Immunological Societies, UniProtKB and Allergome. We extended the hexamer hit rule by removing peptides with high probability of random occurrence measured by sequence entropy as well as requiring 3 or more hexamer hits consistent with natural linear epitope patterns in known allergens. This is complemented with a Gluten-like repeat pattern detection. We also switched from a linear sequence window similarity to a B-cell epitope-like 3D surface similarity window which became possible through extensive 3D structure modeling covering the majority (74%) of allergens. In case no structure similarity is found, the decision workflow reverts to the old linear sequence window rule. The overall accuracy of AllerCatPro is 84% compared with other current methods which range from 51 to 73%. Both the FAO/WHO rules and AllerCatPro achieve highest sensitivity but AllerCatPro provides a 37-fold increase in specificity. AVAILABILITY AND IMPLEMENTATION: https://allercatpro.bii.a-star.edu.sg/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
License type:
http://creativecommons.org/licenses/by/4.0/
Funding Info:
This work has been supported by the Agency of Science, Technology and Research (A*STAR) Singapore and the Procter & Gamble company.
Description:
ISSN:
1367-4803
1460-2059
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