Epitope Screening and Cell Cooperation in the Immune Response

We present a combination of techniques of systems biology and immunoinformatics to simulate the immune response. Amino acid sequences representing molecular binding sites and bioinformatics based predictions of T and B cell epitopes become components of an agent-based simulator. To determine the immunogenic parts of the invading antigen, we resort to existing prediction methods together with a method, which uses Miyazawa and Jernigan protein–protein potential measurements, for assessing molecular binding. A classical immunization experiment is used as benchmark of the resulting model. We also reproduce the affinity maturation phenomena by the emergence of one or more dominating clones of lymphocytes in the situation of chronic exposure to the immunogenic molecule. These results show that the simulator produces a dynamics that is stable and consistent with basic immunological knowledge.