Still SDAPing Along: 20 Years of the Structural Database of Allergenic Proteins

Abstract

The introduction of plant extracts to mitigate the symptoms of “hay fever”, about a century ago, led to discoveries beginning sixty years ago on determining the sequences and eventually structures of allergenic proteins. As more proteins were cloned, there was a need to rapidly identify and categorize those with significant similarity to known allergens. The Structural Database of Allergenic Proteins (SDAP) was created at the beginning of the 21st century as the first cross-referenced website to allow rapid overview of the structures and sequences of allergenic proteins. SDAP provides a way to identify sequence and functional similarities between these proteins, despite the complex nomenclature system based on the Latin names of their different sources. A rapid FASTA search simplifies grouping allergens from the same structural or functional family. SDAP also provides an overview of the rapidly expanding literature on the sequence, structure and epitopes of allergenic proteins and a way to estimate the potential allergenicity of novel proteins based on rules provided by the IUIS. Twenty years and a pandemic later, the list of allergenic proteins and their attributes continues to grow. SDAP is expanding and improving to allow rapid access to all this information.

Allergic to bureaucracy? Regulatory allergenicity assessments of novel food: Motivations, challenges, compromises, and possibilities

“…The data on allergens, including their structures, epitopes, and literature, have increased remarkably due to protein sequencing and advancements in immunological research (Maleki et al., 2022). Homology search is a key component of bioinformatics analyses.…”

“…Furthermore, SDAP enables the generation of three‐dimensional (3D) models by incorporating structural data and templates. It also offers peptide homology search capabilities (Maleki et al., 2022) and allows free access for non‐profit use, although commercial use requires a license. However, SDAP is criticized for its limited coverage of allergens with known crystal structures and solved 3D structures (Ladics, 2018).…”

Food allergen detection by mass spectrometry: From common to novel protein ingredients

“…It has been agreed by several studies [144,145] that putative allergen identification requires either (i) an identity percentage higher than 35% in an 80 aa sequence or (ii) at least 6 identical contiguous aa between a novel food protein and a known allergen. Even though these rules do not apply to conformational allergens, several software programs and dedicated databases are available for similarity comparisons, such as Allergen.org [30], AllFam [146], Allergome [147], Allermatch [148], COMPARE [149], AllergenOnline (AO) [150], Structural Database of Allergenic Proteins (SDAP) [151], Allergen Database for Food Safety [152], and AllerCatPro 2.0 [153]. Unfortunately, the effectiveness of identifying potential cross-reactive allergenic proteins in novel foods is heavily dependent on the reference database used.…”

The updated Structural Database of Allergenic Proteins (SDAP 2.0) provides 3D models for allergens and incorporated bioinformatics tools

“… 3 It is known that allergens from many different sources can cause dangerous cross-reactions, which may be revealed by sequence and structural relationships. 4 , 5 The Structural Database of Allergenic Proteins (SDAP), the first publicly available, cross-referenced database of allergenic proteins, 6 allowed users to rapidly determine relationships between allergens or to any input sequence using specifically designed bioinformatic tools. 7 , 8 Other websites (recently summarized 9 ) with different goals complement this information.…”

“…Bioinformatic tools developed by us and other groups, functioning “on the fly,” allow rapid comparison of allergens according to protein families (Pfams), 11 physicochemical property motifs, 12 physical relationships, and biological functions. 4 , 6 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 The tools now integrated into SDAP 2.0 and, most significantly, 3-dimensional (3D) structures of more than 1600 distinct allergens and their isoforms are a valuable resource for identifying cross-reactive allergens. Recently, a major advance in determining a conformational IgE epitope of the house dust mite allergen Der p 2 in a high-resolution X-ray crystal structure was achieved, 21 which suggests that experimental data as input for our bioinformatics tools for predicting cross-reactivities will be available in increasing numbers.…”