Navigating through the Jungle of Allergens: Features and Applications of Allergen Databases

Abstract

The increasing number of available data on allergenic proteins demanded the establishment of structured, freely accessible allergen databases. In this review article, features and applications of 6 of the most widely used allergen databases are discussed. The WHO/IUIS Allergen Nomenclature Database is the official resource of allergen designations. Allergome is the most comprehensive collection of data on allergens and allergen sources. AllergenOnline is aimed at providing a peer-reviewed database of allergen sequences for prediction of allergenicity of proteins, such as those planned to be inserted into genetically modified crops. The Structural Database of Allergenic Proteins (SDAP) provides a database of allergen sequences, structures, and epitopes linked to bioinformatics tools for sequence analysis and comparison. The Immune Epitope Database (IEDB) is the largest repository of T-cell, B-cell, and major histocompatibility complex protein epitopes including epitopes of allergens. AllFam classifies allergens into families of evolutionarily related proteins using definitions from the Pfam protein family database. These databases contain mostly overlapping data, but also show differences in terms of their targeted users, the criteria for including allergens, data shown for each allergen, and the availability of bioinformatics tools.

WHO/IUIS Allergen Nomenclature: Providing a common language

“…Several publicly available allergen databases exist with different purposes, strengths and weaknesses (reviewed by Radauer, 2017). The WHO/IUIS allergen nomenclature database provides a systematic and official allergen nomenclature for many allergens.…”

Progress in the Analysis of Food Allergens through Molecular Biology Approaches

“…Numerous studies addressed the identification of epitopes (i.e., regions of the allergen recognized by specific antibodies) in allergenic molecules. Identification and characterization of allergen epitopes is a key step for understanding the dynamics of the allergenic immune response and identifying biomarkers or therapeutic targets for specific immunotherapy [32]. Epitopes are generally divided in linear or conformational, depending on whether they correspond to a continuous amino acid sequence or to a group of amino acids variously distributed in the primary structure of the allergen and which are oriented in close proximity within each other in the three-dimensional structure of the folded allergen [33].…”

“…The enormous amount of data produced over the last 30 years on allergens allowed the development of several allergen related databases containing datasets and bioinformatic tools to analyse their structural features (Table 1). Accordingly, the need for a review analysis of such databases also emerged, leading to the publication of several review articles on allergen databases [32,67,68,69,70,71]. In particular, the recent review by Radauer and Breiteneder [68] gives an updated critical analysis of the available databases, including their characteristics, strengths and weakness.…”

Integrated approaches in diagnostics and therapy of allergic diseases

“…Поисковые и программные сред-ства для этой цели были разработаны и внедре-ны, в частности, в Структурную базу данных ал-лергенных белков (SDAP) [14]. SDAP содержит информацию о более чем 800 аллергенах и об-ширные библиографические ссылки на другие общедоступные базы данных.…”