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.
Keywords: Alignment-independent methods; Allergenicity; Allergenicity prediction; Physicochemical properties of amino acids.