IEDB-3D 2.0: Enabling visualization of epitopes on the 3D structure of the corresponding antigens

Abstract The Immune Epitope Database and Analysis Resource (IEDB) contains information related to antibodies, T cells, and MHC across a broad spectrum of research fields (infectious diseases, cancer, allergy, autoimmunity, and transplantation). A critical component of this information is three-dimensional structural data on T cell receptors (TCRs), antibodies, and pairwise residue interactions between immune receptors and antigens, which we refer to as IEDB-3D. Analysis using atomic models helps to understand the intricate interactions between immune receptor and epitopes. Here, we present IEDB-3D 2.0, which incorporates a complete overhaul of how we obtain and present 3D structural data from PDB and AlphaFold database. We implemented a new molecule visualizer, iCn3D, to replace outdated java-based technology. In addition, we have designed a new epitope mapping system that matches each epitope available in the IEDB with its antigen structural data. Lastly, we integrated our epitope mapping system with immunogenic data retrieved from the IEDB’s ImmunomeBrowser, which now can be used to highlight immunogenic regions of an antigen directly in iCn3D. Overall, the IEDB-3D 2.0 provides an updated tool platform to visualize epitope data cataloged in the IEDB. Research reported in this publication was supported by the National Institutes of Health contract 75N93019C00001 and grant U24CA248138.