Immune system simulation online

Nicolas Rapin; Ole Lund; Filippo Castiglione

doi:10.1093/bioinformatics/btr335

Immune system simulation online

Nicolas Rapin
, Ole Lund
, Filippo Castiglione

National Research Council of Italy

Research output: Contribution to journal › Journal article › Research › peer-review

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. AVAILABILITY: http://www.cbs.dtu.dk/services/C-ImmSim-10.1/ CONTACT: [email protected]

Original language	English
Journal	Bioinformatics
Volume	27
Issue number	14
Pages (from-to)	2013-2014
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btr335
Publication status	Published - 2011

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http://bioinformatics.oxfordjournals.org/content/27/14/2013

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title = "Immune system simulation online",

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{\textendash}peptide complex calculated as the averaged sum of a residue{\textendash}residue contact potential. These steps are executed for all lymphocytes agents encountering the antigen in a wide-reaching Monte Carlo simulation. AVAILABILITY: http://www.cbs.dtu.dk/services/C-ImmSim-10.1/ CONTACT: [email protected]",

author = "Nicolas Rapin and Ole Lund and Filippo Castiglione",

year = "2011",

doi = "10.1093/bioinformatics/btr335",

language = "English",

volume = "27",

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T1 - Immune system simulation online

AU - Rapin, Nicolas

AU - Lund, Ole

AU - Castiglione, Filippo

PY - 2011

Y1 - 2011

N2 - 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. AVAILABILITY: http://www.cbs.dtu.dk/services/C-ImmSim-10.1/ CONTACT: [email protected]

AB - 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. AVAILABILITY: http://www.cbs.dtu.dk/services/C-ImmSim-10.1/ CONTACT: [email protected]

U2 - 10.1093/bioinformatics/btr335

DO - 10.1093/bioinformatics/btr335

M3 - Journal article

C2 - 21685045

SN - 1367-4803

VL - 27

SP - 2013

EP - 2014

JO - Bioinformatics

JF - Bioinformatics

IS - 14

ER -

Immune system simulation online

Abstract

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