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Updated: Aug 9, 2025

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

Published on: March 25, 2014

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

Marcus Mendes¹, Jarjapu Mahita¹, Nina Blazeska¹

¹Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA.

Protein Science : a Publication of the Protein Society

|February 22, 2023

Summary

This summary is machine-generated.

The Immune Epitope Database (IEDB) now offers IEDB-3D 2.0, an updated platform for visualizing 3D structural data of immune interactions. This enhanced tool improves understanding of receptor:ligand mechanics in immunity and disease.

Keywords:

adaptive immunity antigens database epitopes immunoinformatics structural biology

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Area of Science:

Immunoinformatics
Structural Biology
Computational Biology

Background:

The Immune Epitope Database (IEDB) is a key resource for immunological data, including structural information on immune receptors and their ligands.
Three-dimensional (3D) structural data (IEDB-3D) is crucial for understanding the mechanics of receptor-ligand interactions in immunity.
Existing visualization tools for IEDB-3D data were outdated and limited.

Purpose of the Study:

To present IEDB-3D 2.0, a comprehensive update to the IEDB's 3D structural data visualization capabilities.
To introduce a new, modern 3D viewer and an improved epitope mapping system.
To integrate immunogenicity data for enhanced visualization of key antigenic regions.

Main Methods:

Overhauled data acquisition and presentation pipelines for 3D structural information.
Implemented iCn3D as a new, interactive 3D viewer, replacing older Java-based technology.
Developed a novel epitope mapping system linking IEDB epitopes to corresponding antigen structures.
Integrated immunogenicity data from ImmunomeBrowser for direct visualization within iCn3D.

Main Results:

IEDB-3D 2.0 offers a significantly improved user experience for exploring 3D structural data.
The new epitope mapping system accurately associates epitopes with their structural contexts.
Direct visualization of immunogenic regions on antigen structures is now possible within iCn3D.
The updated platform enhances the utility of IEDB structural data for researchers.

Conclusions:

IEDB-3D 2.0 represents a major advancement in visualizing and analyzing 3D epitope data.
The new tools facilitate a deeper mechanistic understanding of immune receptor-ligand interactions.
This updated platform will accelerate research in infectious diseases, allergies, autoimmunity, and transplantation by providing better access to structural immunological data.