Journal
BIOINFORMATICS
Volume 27, Issue 14, Pages 2013-2014Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btr335
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Funding
- EC [FP6-2004-IST-4, 028069]
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Motivation: The recognition of antigenic peptides is a major event of an immune response. In current mesoscopic-scale simulators of the immune system, this crucial step has been modeled in a very approximated way. Results: We have equipped an agent-based model of the immune system with immuno-informatics methods to allow the simulation of the cardinal events of the antigenic recognition, going from single peptides to whole proteomes. The recognition process accounts for B cell-epitopes prediction through Parker-scale affinity estimation, class I and II HLA peptide prediction and binding through position-specific scoring matrices based on information from known HLA epitopes prediction tools, and TCR binding to HLA-peptide complex calculated as the averaged sum of a residue-residue contact potential. These steps are executed for all lymphocytes agents encountering the antigen in a wide-reaching Monte Carlo simulation.
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