title: Immune system simulation online.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  http://www.cbs.dtu.dk/services/C-ImmSim-10.1/
authors.affiliation: Biotech Research & Innovation Centre and Bioinformatics Centre, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Rapin
authors.forename: Ole
authors.initials: O
authors.lastname: Lund
authors.forename: Filippo
authors.initials: F
authors.lastname: Castiglione
mesh_terms: D003198:Computer Simulation; D018604:Epitope Mapping / Q000379:methods; D006801:Humans; D007107:Immune System; D020407:Internet; D008214:Lymphocytes; D008954:Models, Biological; D009862:Online Systems; D056510:Position-Specific Scoring Matrices; D013223:Statistics as Topic