An Alignment-Independent Platform for Allergenicity Prediction

Part of the Methods in Molecular Biology book series (MIMB, volume 2131)


A great number of novel proteins have been generated from new sources and genetically modified foods during the last decade. As the allergenicity of these proteins is of particular importance for their safe usage, fast and reliable screening strategies for allergenicity assessment are required. The WHO/FAO guidance directs to structural similarities between the novel proteins and known allergens detected by sequence alignment. However, the allergic response involves conformational IgE epitopes that are undetectable by sequence alignment. Here, we present a protocol for allergenicity prediction based on a platform of three alignment-independent servers developed in our lab: AllerTOP v.1, AllerTOP v.2, and AllergenFP. The servers use similar datasets but different chemical descriptors and methods to derive models for allergenicity prediction. The platform is freely accessible and user-friendly. The protocol is demonstrated stepwise on a randomly chosen query protein.

Key words

Allergenicity Allergenicity prediction Physicochemical properties of amino acids Alignment-independent methods 



This work has been accomplished with the financial support by the Grant No BG05M2OP001-1.001-0003, financed by the Science and Education for Smart Growth Operational Program (2014-2020), and co-financed by the European Union through the European structural and investment funds.


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© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Faculty of PharmacyMedical University of SofiaSofiaBulgaria

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