Dataset Information

IEDB-3D 2.0: Structural data analysis within the Immune Epitope Database.

ABSTRACT: The Immune Epitope Database (IEDB) catalogs T cell, B cell, and major histocompatibility complex ligand information in the context of infectious disease, allergy, autoimmunity, and transplantation. An important component of this information is three-dimensional structural data on T cell receptors, antibodies, and pairwise residue interactions between immune receptors and antigens, which we refer to as IEDB-3D. Such data is highly valuable for mechanically understanding receptor:ligand interactions. Here, we present IEDB-3D 2.0, which comprises a complete overhaul of how we obtain and present 3D structural data. A new 3D viewer experience that utilizes iCn3D has been implemented to replace outdated java-based technology. In addition, we have designed a new epitope mapping system that matches each epitope available in the IEDB with its antigen structural data. Finally, immunogenicity data retrieved from the IEDB's ImmunomeBrowser can now be used to highlight immunogenic regions of an antigen directly in iCn3D. Overall, the IEDB-3D 2.0 provides an updated tool platform to visualize epitope data cataloged in the IEDB.

SUBMITTER: Mendes M

PROVIDER: S-EPMC10022491 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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IEDB-3D 2.0: Structural data analysis within the Immune Epitope Database.

Mendes Marcus M Mahita Jarjapu J Blazeska Nina N Greenbaum Jason J Ha Brendan B Wheeler Kelly K Wang Jiyao J Shackelford Deborah D Sette Alessandro A Peters Bjoern B

Protein science : a publication of the Protein Society 20230401 4

The Immune Epitope Database (IEDB) catalogs T cell, B cell, and major histocompatibility complex ligand information in the context of infectious disease, allergy, autoimmunity, and transplantation. An important component of this information is three-dimensional structural data on T cell receptors, antibodies, and pairwise residue interactions between immune receptors and antigens, which we refer to as IEDB-3D. Such data is highly valuable for mechanically understanding receptor:ligand interactio ...[more]

PMID: 36806329

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Project description:BackgroundAllergenic 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.ObjectiveWe 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.MethodsPreviously 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.ResultsA 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.ConclusionsSDAP 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.

Dataset Information

IEDB-3D 2.0: Structural data analysis within the Immune Epitope Database.

Publications

IEDB-3D 2.0: Structural data analysis within the Immune Epitope Database.

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