Immune epitope database analysis resource (IEDB-AR)

Abstract

We present a new release of the immune epitope database analysis resource (IEDB-AR, http://tools.immuneepitope.org), a repository of web-based tools for the prediction and analysis of immune epitopes. New functionalities have been added to most of the previously implemented tools, and a total of eight new tools were added, including two B-cell epitope prediction tools, four T-cell epitope prediction tools and two analysis tools.

Figure 1.

Performances of prediction methods measured using either cross-validation or independent data set. Each data point represents an area under a receiver-operating-characteristic curve (AUC) for an MHC molecule (and its preferred peptide length). AUCs generated using cross-validation were taken from ref. (6), while those using independent data set are presented here for the first time. For independent data set, prediction methods trained on the old data used in ref. (6) were tested on the new, and thus independent, peptide-binding data that recently became available. In the case of cross-validation, however, an AUC value is an average of AUCs generated by training a prediction method on 4/5 of a data set and testing on the remaining one. Each data set for an MHC molecule had at least 50 binding affinity measurements.

Figure 2.

Screenshot of the ‘3D View’ page for the DiscoTope tool on IEDB-AR. The input for this prediction is the PDB structure file of AMA1 from Plasmodium falciparum (28) (PDB ID 1Z40). On the left is the 3D display of this structure, with all predicted epitope residues for chain A highlighted in yellow. The table on the right lists details of these predicted residues. Clicking on the ‘CPK’ button in the table highlights that specific residue in the 3D display, as seen on the top.

Figure 3.

Screenshot of the EpitopeViewer 2.0 showing the 26-2F epitope of human angiogenin [PDB ID: 1H0D, chain C] in red (the rest of the antigen is invisible) and paratope in yellow in CPK representation. The distance between the atom N of residue 34 Gly and atom Cα of residue 91 Pro of the epitope is 14.23 Å (red line).