The design and implementation of the immune epitope database and analysis resource

Abstract

Epitopes are defined as parts of antigens interacting with receptors of the immune system. Knowledge about their intrinsic structure and how they affect the immune response is required to continue development of techniques that detect, monitor, and fight diseases. Their scientific importance is reflected in the vast amount of epitope-related information gathered, ranging from interactions between epitopes and major histocompatibility complex molecules determined by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines. Our goal is to provide a central resource capable of capturing this information, allowing users to access and connect realms of knowledge that are currently separated and difficult to access. Here, we portray a new initiative, "The Immune Epitope Database and Analysis Resource." We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide.

Fig. 1

Orthogonal views of X-ray structures of immunological complexes available in the Protein Data Bank. a Complex of a human TR, influenza Ha antigen peptide PKYVKQNTLKLAT, and MHC Class II HLA-DR1 (PDB ID, 1fyt). T-cell epitope residues colored in orange. b Xenoreactive complex AHIII 12.2 TR bound to P1049 ALWGFFPVLS and MHC Class I HLA-A2.1 (PDB ID, 1lp9). T-cell epitope residues colored in orange. c IgG1 Fab fragment of E8 antibody complexed with horse cytochrome c (PDB ID, 1wej). B cell epitope and paratope residues colored in red and green, accordingly. The figures were obtained using the WebLab viewer

Fig. 2

Class diagram for the Immune Epitope Database and Analysis Resource

Fig. 3

The curation process