Negi Surendra S, Schein Catherine H, Braun Werner
Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Tex.
Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Tex.
J Allergy Clin Immunol Glob. 2023 Aug 11;2(4):100162. doi: 10.1016/j.jacig.2023.100162. eCollection 2023 Nov.
Allergenic proteins can cause IgE-mediated adverse reactions in sensitized individuals. Although the sequences of many allergenic proteins have been identified, bioinformatics data analysis with advanced computational methods and modeling is needed to identify the basis for IgE binding and cross-reactivity.
We aim to present the features and use of the updated Structural Database of Allergenic Proteins 2.0 (SDAP 2.0) webserver, a unique, publicly available resource to compare allergens using specially designed computational tools and new high-quality 3-D models for most known allergens.
Previously developed and novel software tools for identifying cross-reactive allergens using sequence and structure similarity are implemented in SDAP 2.0. A comprehensive set of high-quality 3-D models of most allergens was generated with the state-of-the-art AlphaFold 2 software. A graphics tool enables the interactive visualization of IgE epitopes on experimentally determined and modeled 3-D structures.
A user can search for allergens similar to a given input sequence with the FASTA algorithm or the window-based World Health Organization/International Union of Immunological Societies (WHO/IUIS) guidelines on safety concerns of novel food products. Peptides similar to known IgE epitopes can be identified with the property distance tool and conformational epitopes by the Cross-React method. The updated database contains 1657 manually curated sequences including all allergens from the IUIS database, 334 experimentally determined X-ray or NMR structures, and 1565 3-D models. Each allergen/isoallergen is classified according to its protein family.
SDAP provides access to the steadily increasing information on allergenic structures and epitopes with integrated bioinformatics tools to identify and analyze their similarities. In addition to serving the research and regulatory community, it provides clinicians with tools to identify potential coallergies in a sensitive patient and can help companies to design hypoallergenic foods and immunotherapies.
变应原蛋白可在致敏个体中引发IgE介导的不良反应。尽管许多变应原蛋白的序列已被鉴定,但仍需要使用先进的计算方法和建模进行生物信息学数据分析,以确定IgE结合和交叉反应的基础。
我们旨在介绍更新后的变应原蛋白结构数据库2.0(SDAP 2.0)网络服务器的特点和用途,这是一个独特的、公开可用的资源,可使用专门设计的计算工具和针对大多数已知变应原的新的高质量三维模型来比较变应原。
SDAP 2.0中实现了以前开发的以及用于使用序列和结构相似性识别交叉反应性变应原的新型软件工具。使用最先进的AlphaFold 2软件生成了一套全面的大多数变应原的高质量三维模型。一个图形工具能够在实验确定的和建模的三维结构上交互式可视化IgE表位。
用户可以使用FASTA算法或基于窗口的世界卫生组织/国际免疫学会联盟(WHO/IUIS)关于新型食品安全性问题的指南搜索与给定输入序列相似的变应原。可以使用属性距离工具识别与已知IgE表位相似的肽,并通过交叉反应方法识别构象表位。更新后的数据库包含1657条人工整理的序列,包括来自IUIS数据库的所有变应原、334个实验确定的X射线或核磁共振结构以及1565个三维模型。每个变应原/同种变应原根据其蛋白家族进行分类。
SDAP通过集成生物信息学工具提供了对不断增加的变应原结构和表位信息的访问,以识别和分析它们的相似性。除了为研究和监管界服务外,它还为临床医生提供工具,以识别敏感患者中潜在的共同变应原,并可帮助公司设计低变应原性食品和免疫疗法。