Immunoinformatics comes of age

Abstract

With the burgeoning immunological data in the scientific literature, scientists must increasingly rely on Internet resources to inform and enhance their work. Here we provide a brief overview of the adaptive immune response and summaries of immunoinformatics resources, emphasizing those with Web interfaces. These resources include searchable databases of epitopes and immune-related molecules, and analysis tools for T cell and B cell epitope prediction, vaccine design, and protein structure comparisons. There is an agreeable synergy between the growing collections in immune-related databases and the growing sophistication of analysis software; the databases provide the foundation for developing predictive computational tools, which in turn enable more rapid identification of immune responses to populate the databases. Collectively, these resources contribute to improved understanding of immune responses and escape, and evolution of pathogens under immune pressure. The public health implications are vast, including designing vaccines, understanding autoimmune diseases, and defining the correlates of immune protection.

Figure 1. Interaction of an Epitope with an MHC Class I Protein

Ribbon representation of the 1.65 Å resolution X-ray crystal structure of the MHC I allele B*5703 in complex with the KAF-11 peptide (KAFSPEVIPMF) derived from the HIV-1 p24 capsid protein. The blue ribbon indicates the alpha chain, the red chain is beta-2 microglobulin, and the molecule in the binding cleft is the antigenic peptide. The red and blue-green spheres mark the alpha carbons of the canonical peptide-binding B- and F-pocket residues, respectively. The green spheres represent the alpha carbons of the peptide anchor residues at P2 and P11.