Useful Tools in Immunology: The Immune Epitope Database

The Immune Epitope Database (IEDB) is a free online resource established by the National Institute for Health. The IEDB makes it easy for scientists and researchers to search for experimental data characterizing antibody and T cell epitopes for allergens, infectious diseases, autoimmune diseases, and transplants/alloantigens. Beyond epitope search, the IEDB also offers unique epitope analysis and prediction tools.

The IEDB has curated hundreds of thousands of journal articles and author submissions and organizes the epitope data in an easy-to-read, easy-to-search, easy-to-sort table format. New articles are typically added to the database within eight weeks of publication. Here are the updated IEDB statistics as of October 2018:

Who Should Use the IEDB?

This database is best suited for advanced, PhD-level scientists working in immunology or vaccine development. Postdocs, senior scientists, principal investigators, and directors will find the IEDB most useful.

We use the IEDB when we begin development of a new T cell line to select the best epitope for the antigen of interest. It saves time when we know we are working with a peptide that has been reported in the scientific literature or at least is predicted to bind well to a given HLA allele. We have also used the IEDB to design antigens for immunization and antibody development to increase success and specificity.

3 Ways to Use the IEDB

1. Basic Epitope Search

The IEDB homepage is designed to facilitate the most commonly used search queries by immunologists. It’s easy to get started; just select the parameters you are interested in, including:

Epitope Sequence

  • Any Epitopes
  • Linear Epitope (Exact Match, Substring, Blast 90%, Blast 80%, Blast 70%)
  • Discontinuous Epitopes
  • Non-Peptidic Epitopes

Antigen

  • Organism
  • Antigen Name

Host

  • Any Host
  • Humans
  • Mice
  • Non-Human Primates

Assay

  • Positive Assays Only
  • T Cell Assays
  • B Cell Assays
  • MHC Ligand Assays

MHC Restriction

  • Any MHC Restriction
  • MHC Class I
  • MHC Class II
  • MHC Nonclassical

Disease

  • Any Disease
  • Infectious Disease
  • Allergic Disease
  • Autoimmune Disease

 

From the results page, you can implement additional filters and see the epitopes, antigens, assays, and references that match your search parameters. Easily sort the data and export what you need into Excel.  

2. B or T Cell Epitope Prediction

The IEDB also offers an algorithm for predicting B cell and T cell epitopes.

The T Cell Epitope Prediction tool scans antigen sequences for amino patterns that indicate MHC I or II binding, MHC I processing (how the protein will be digested in the proteasome), and MHC I immunogenicity.

Here is an example output of the MHC I Processing prediction tool for HPV E6 protein, showing the top 10 epitopes for the HLA-A*02:01 allele.

StartEndLengthPeptideProteasome ScoreTAP ScoreMHC ScoreProcessing ScoreTotal ScoreMHC IC50
18269KLPQLCTEL1.410.52-2.361.93-0.43227
526110FAFRDLCIVY1.941.24-3.813.18-0.636485.2
52609FAFRDLCIV1.040.11-2.061.15-0.91115
486114EVYDFAFRDLCIVY1.941.38-4.233.32-0.9117177.7
334513IILECVYCKQQLL1.410.43-2.941.84-1.11877.3
53619AFRDLCIVY1.941.38-4.513.32-1.1832065.6
293810TIHDIILECV1.110.2-2.511.31-1.2320.2
506112YDFAFRDLCIVY1.941.2-4.363.14-1.2222940.5
496113VYDFAFRDLCIVY1.941.26-4.453.2-1.2428067
516111DFAFRDLCIVY1.941.19-4.433.13-1.327088.7

The B Cell Epitope Prediction tool works similarly to predict regions of proteins that are likely to be recognized as epitopes during B cell response. The IEDB predicts linear B cell epitopes using antigen sequence properties and predicts discontinuous B cell epitopes using Discotope and ElliPro. 

3. Additional Epitope Analysis

You can run further analysis on a specific epitope sequence or group of sequences using the IEDB’s database and specialized analysis tools for:

  • Population Coverage
  • Epitope Conservancy Analysis
  • Epitope Cluster Analysis

 

Questions About the IEDB?

The website has a list of common queries along with a series of how-to videos that explain the tools in more detail. We hope you find the IEDB a useful tool for immunology research!

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