Abstract
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.
| Original language | English |
|---|---|
| Journal | Bioinformatics |
| Volume | 27 |
| Issue number | 14 |
| Pages (from-to) | 2013-4 |
| Number of pages | 2 |
| ISSN | 1367-4803 |
| DOIs | |
| Publication status | Published - Jul 2011 |
Keywords
- Computer Simulation
- Epitope Mapping
- Humans
- Immune System
- Internet
- Lymphocytes
- Models, Biological
- Online Systems
- Position-Specific Scoring Matrices
- Statistics as Topic