Humoral immune responses are mediated through antibodies. About 1010 to 1012 different antigen binding sites called paratopes are generatedby genomic recombination. These antibodies are capable to bind to a variety of structures ranging from small molecules to protein complexes,including any posttranslational modification thereof. When studying protein-antibody interactions, two types of epitopes (the region paratopesinteract with) are to be distinguished from each other: i) conformational and ii) linear epitopes. All potential linear epitopes of a protein can berepresented by short peptides derived from the primary amino acid sequence. These peptides can be synthesized and arrayed on solid supports,e.g. glass slides (see Lorenz et al., 2009 [1]). By incubating these peptide arrays with antibody mixtures such as human serum or plasma,peptides can be determined that interact with antibodies in a specific fashion.The training set of this challenge comprises sequences of peptides that either bind intravenous immunoglobulin (IVIg) antibodies with highaffinity/avidity (positive training set) or do not (negative training set). The challenge consists of determining for each peptide within the test setwhether its reactivity with antibodies is strong or weak. Any approach that predicts the specificity scores of each peptide can in principle beapplied for stratifying peptides presented in the test set into binders (to antibodies) and non-binders. Any publicly accessible information availablefor studying protein-protein-interactions as well as any approach enabling the determination of rule sets for predicting peptide-antibody affinitiesmight be applied.
