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, 40 (Web Server issue), W525-30

Immune Epitope Database Analysis Resource


Immune Epitope Database Analysis Resource

Yohan Kim et al. Nucleic Acids Res.


The immune epitope database analysis resource (IEDB-AR: is a collection of tools for prediction and analysis of molecular targets of T- and B-cell immune responses (i.e. epitopes). Since its last publication in the NAR webserver issue in 2008, a new generation of peptide:MHC binding and T-cell epitope predictive tools have been added. As validated by different labs and in the first international competition for predicting peptide:MHC-I binding, their predictive performances have improved considerably. In addition, a new B-cell epitope prediction tool was added, and the homology mapping tool was updated to enable mapping of discontinuous epitopes onto 3D structures. Furthermore, to serve a wider range of users, the number of ways in which IEDB-AR can be accessed has been expanded. Specifically, the predictive tools can be programmatically accessed using a web interface and can also be downloaded as software packages.


Figure 1.
Figure 1.
Screenshot of the peptide:MHC-I binding predictive tool results page generated using the ‘IEDB recommended’ option. The first highlighted area at the top indicates a checkbox with which the user can expand the table to display method-specific predictions. The second highlighted area at the bottom allows the user to download the prediction results as a text file.
Figure 2.
Figure 2.
Screenshots of the homology modeling tool. (A) The input page. (B) The output page: a pair-wise sequence alignment of the source protein and one of the PDB hits. Epitope residues are shown in orange. Solvent exposed residues (with a relative solvent accessibility of side chain atoms, RSA, above 40%) are shown in red and buried (RSA below 7%), in blue (these cut-offs can be changed as shown in C). In the annotation for secondary structures (34), ‘H’ denotes an alpha-helix; ‘G’, a 3-10 helix; ‘E’, a beta-strand; ‘T’, a turn; ‘X’, no structure. (C) The output page: a fragment of a multiple sequence alignment of the source protein and all PDB hits (at the Blast E-value < 1.0E-3). (D) Default view of the protein source and epitope (colored in blue) in EpitopeViewer. The view can be changed using the EpitopeViewer’s tools and shortcuts accessible on the right top panel.

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