Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 40 (Web Server issue), W525-30

Immune Epitope Database Analysis Resource

Affiliations

Immune Epitope Database Analysis Resource

Yohan Kim et al. Nucleic Acids Res.

Abstract

The immune epitope database analysis resource (IEDB-AR: http://tools.iedb.org) 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.

Figures

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.

Similar articles

See all similar articles

Cited by 126 articles

See all "Cited by" articles

References

    1. Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui H-H, Buus S, Frankild S, Greenbaum J, et al. Immune epitope database analysis resource (IEDB-AR) Nucleic. Acids Res. 2008;36:W513–W518. - PMC - PubMed
    1. Kim Y, Sidney J, Pinilla C, Sette A, Peters B. Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior. BMC Bioinformatics. 2009;10:394. - PMC - PubMed
    1. Peters B, Sette A. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics. 2005;6:132. - PMC - PubMed
    1. Hoof I, Peters B, Sidney J, Pedersen L, Sette A, Lund O, Buus S, Nielsen M. NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics. 2009;61:1–13. - PMC - PubMed
    1. Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, Buus S, Brunak S, Lund O. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci. 2003;12:1007–1017. - PMC - PubMed

Publication types

MeSH terms

Substances

Feedback