IEDB-3D

IEDB-3D catalogs and analyzes three-dimensional structures of B-cell and T-cell epitopes and MHC ligands from Protein Data Bank (PDB) antibody, T-cell receptor, and MHC complexes to support structural immunology research.

Key Features:

• Comprehensive Cataloging: Compiles B- and T-cell epitopes and MHC ligands associated with antibody, T-cell receptor (TCR), and MHC complexes present in the Protein Data Bank (PDB).
• Curated Scientific Literature: Links PDB structures to primary journal citations and curates epitope annotations and associated functional assay information from the literature.
• Calculated Structural Data: Provides calculated intermolecular contacts and interface area measurements for each cataloged structure.
• Visualization Tools: Includes EpitopeViewer for three-dimensional visualization of epitopes and their complexes.
• Integrated Search Capabilities: Integrated within the IEDB framework to enable queries across curated and calculated structural data using criteria such as pathogen, immune response elicited, or immune system component.
• Data Export Options: Supports export of query results in Microsoft Excel format and bulk downloads of curated and calculated data in XML or MySQL formats.

Scientific Applications:

• Antigen and vaccine design: Provides structural epitope information to inform antigen design and vaccine development efforts.
• Therapeutic antibody engineering: Informs therapeutic antibody engineering through analysis of antibody–epitope interface contacts and interface areas.
• Mechanistic studies of immune recognition: Enables investigation of the molecular basis of epitope recognition by antibodies, TCRs, and MHC molecules.
• Structural immunology research: Facilitates integration of PDB structural data with epitope and assay annotations for structural immunology studies.

Methodology:

Cataloging of PDB antibody/TCR/MHC complexes and curation of primary citations and epitope/assay annotations; calculation of intermolecular contacts and interface areas; 3D visualization via EpitopeViewer; searchable integration within IEDB and export in Excel, XML, or MySQL formats.