Immune system simulation online

Nicolas Philippe Jean-Pierre Rapin; Ole Lund; Filippo Castiglione

doi:10.1093/bioinformatics/btr335

Immune system simulation online

Nicolas Philippe Jean-Pierre Rapin, Ole Lund, Filippo Castiglione

Bioinformatik og RNA Biologi

18 Citationer (Scopus)

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.

Originalsprog	Engelsk
Tidsskrift	Bioinformatics
Vol/bind	27
Udgave nummer	14
Sider (fra-til)	2013-4
Antal sider	2
ISSN	1367-4803
DOI	https://doi.org/10.1093/bioinformatics/btr335
Status	Udgivet - jul. 2011

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10.1093/bioinformatics/btr335

Citationsformater

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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-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.",

keywords = "Computer Simulation, Epitope Mapping, Humans, Immune System, Internet, Lymphocytes, Models, Biological, Online Systems, Position-Specific Scoring Matrices, Statistics as Topic",

author = "Rapin, {Nicolas Philippe Jean-Pierre} and Ole Lund and Filippo Castiglione",

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T1 - Immune system simulation online

AU - Rapin, Nicolas Philippe Jean-Pierre

AU - Lund, Ole

AU - Castiglione, Filippo

PY - 2011/7

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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.

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.

KW - Computer Simulation

KW - Epitope Mapping

KW - Humans

KW - Immune System

KW - Internet

KW - Lymphocytes

KW - Models, Biological

KW - Online Systems

KW - Position-Specific Scoring Matrices

KW - Statistics as Topic

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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