Database Overview
The Immune Epitope Database (IEDB, iedb.org), funded by NIAID, was established in 2004 as a free resource to house experimental data related to adaptive immune epitopes, and to also provide leading-edge epitope analysis and prediction tools. Over the past 20 years, the IEDB has extracted antibody, T cell, and major histocompatibility complex (MHC) experimental data from >25,000 publications, amounting to 6.8 million assays and 1.6 million immune structures. The scope of the IEDB includes data related to infectious, allergic, autoimmune, and transplant diseases in vertebrate hosts. Linear and discontinuous peptidic epitopes, as well as non-peptidic epitopes, are included, along with receptor information where available.
To be included in the IEDB, epitopes must meet the following criteria:
- Linear peptides must be less than 50 amino acids in length
- Discontinuous residues must be shown to be important in recognition
- Non-peptidic epitopes must be less than 5,000 Daltons
- Epitope must be tested as an immunogen or an antigen
- Minimal information about the epitope, such as the sequence, structure, or host, is provided
Collaboration with Ontologies
A key element of the database and the curation strategy is the collaboration with different ontologies, which provides a standardized way to refer to objects and facilitates interoperability between different resources. External ontologies utilized by the IEDB include NCBI, which we rely on for organism classification and taxonomy; and GenBank (or UniProt), which we rely on for protein metadata. By providing finders with accurate and standardized information, we enhance the user experience, improve consistency and accuracy of curation, and facilitate to detect and correct errors.
Literature Curation
A new query of PubMed and the PDB is performed every two weeks to ensure that the IEDB remains up to date with the most relevant scientific literature. Any references associated with potentially curatable information that are not currently in the IEDB’s tracking system are run through an automated document classifier, which determines which references are likely to be curatable based on text recognition, and assigns them a category based on disease type. These are then reviewed by the Curation Team Leader, Dr. Alessandro Sette, to validate classification and curatability. References that have been confirmed to be likely curatable by both the automated and manual scans are then assigned to a curator, who reads the entire reference and either curates it for promotion into the database or deems it uncuratable, based on specific criteria described in more detail in the curation manual and in accordance with our defined practices and procedures. All curators are PhD level scientists with expertise in immunology, and each curation is peer reviewed by another curator before being promoted to the database. Additional quality control measures to ensure that there is consistency and reproducibility in the data available on the IEDB include input from external immunological experts and built-in validation in the curation application.
The curated scientific literature covers articles from 1954 to the present day. Our data reflects the literature and is dependent upon what topics and research scenarios are published. For example, at the start of the COVID pandemic, the IEDB only had data on SARS-CoV1 epitopes. However, now we have 4.6 times the number of publications on SARS-CoV2 compared to CoV1, as new data was rapidly published. While the number of references curated in the IEDB has largely maintained stable per year, the number of assays added per year has massively increased, with the greatest growth seen in MHC assays.
The IEDB also accepts submission data from the research community. More information about this process can be found here.
Querying the IEDB
The IEDB serves multiple distinct user communities, including those studying antibody or T cell responses or MHC ligands. To meet the needs of our users, we have a number of search options available. The Home Page Search article can help you get started, and is focused on the most commonly asked queries by immunologists. For more in-depth information regarding the home page features and the IEDB’s content, refer to the following:
- IEDB Epitopes
- IEDB Assay Types
- Epitope Source
- MHC Restriction and Allele Finder
- Host Search
- Diseases in the IEDB
- TCR and Antibody Sequence Data
- Immunome Browser 3.0
- Using Browse by 3D Structure
For more help with getting started with IEDB queries, a video overview can be found here.
Using the IEDB Analysis Resource
The Immune Epitope Database Analysis Resource (IEDB-AR) is a companion website to the IEDB that provides computational tools focused on the prediction and analysis of B and T cell epitopes. All of the tools are freely available through the public website and many are also available through a REST API and/or a downloadable command-line tool. A virtual machine image of the entire site is also freely available for non-commercial use and contains most of the tools on the public site.
For each tool, a sequence can be entered in FASTA format or as whitespace-separated sequences in a free text box, and a prediction method can be selected. The IEDB recommended prediction methods, which are chosen based on regularly conducted benchmarking efforts, show up at the top of the “Prediction Method” dropdown menu. Once other parameters have been selected, the results can be downloaded. More information on IEDB tools can be found in the IEDB Knowledgebase.
In 2023, the Next-Generation IEDB tools site was launched with the goals of simplifying the user experience, enhancing existing functionality, adding new functionality, ensuring consistency among the tools, and improving the layout and aesthetics of the tools site. The first public release focused on T cell Class I epitope prediction, cluster analysis, and PEPMatch tools, while the second release focused on the cancer specific Mutated Peptide Generator, Peptide Variant Comparison, and PepX tools. The releases of other tools on the NGT site, which are planned for 2025, include T cell Class II and B cell prediction tools. For more information about using the NGT tools site and its featured, refer to the documentation here.
Contact and the Solutions Center
The newly redesigned IEDB solutions center was launched in 2025 with the goal of improving the user experience and organizing IEDB-related content in a way that is more intuitive. Relevant topics are sorted into broad categories, and are tagged with keywords for greater searchability. Another key goal of the redesign was to simplify troubleshooting via the Discussions forum, where any user can post a topic and get feedback from both IEDB staff and the user community, as well as referring to previously posted questions.
If you have any other questions or inquiries, you can contact the IEDB at help@iedb.org.