{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T07:27:01Z","timestamp":1784359621448,"version":"3.55.0"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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\u2013peptide complex calculated as the averaged sum of a residue\u2013residue contact potential.<\/jats:p>\n               <jats:p>These steps are executed for all lymphocytes agents encountering the antigen in a wide-reaching Monte Carlo simulation.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.cbs.dtu.dk\/services\/C-ImmSim-10.1\/<\/jats:p>\n               <jats:p>Contact: \u00a0f.castiglione@iac.cnr.it<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr335","type":"journal-article","created":{"date-parts":[[2011,6,18]],"date-time":"2011-06-18T04:15:07Z","timestamp":1308370507000},"page":"2013-2014","source":"Crossref","is-referenced-by-count":220,"title":["Immune system simulation online"],"prefix":"10.1093","volume":"27","author":[{"given":"Nicolas","family":"Rapin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ole","family":"Lund","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Filippo","family":"Castiglione","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,6,17]]},"reference":[{"key":"2023012712454217600_B1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/0167-5699(92)90135-T","article-title":"A computer model of cellular interactions in the immune system","volume":"13","author":"Celada","year":"1992","journal-title":"Immunol. Today"},{"key":"2023012712454217600_B2","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1006\/jmbi.1996.0114","article-title":"Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading","volume":"256","author":"Miyazawa","year":"1996","journal-title":"J. Mol. Biol."},{"key":"2023012712454217600_B3","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1007\/s00251-008-0330-2","article-title":"MHC motif viewer","volume":"60","author":"Rapin","year":"2008","journal-title":"Immunogenetics"},{"key":"2023012712454217600_B4","doi-asserted-by":"crossref","first-page":"e9862","DOI":"10.1371\/journal.pone.0009862","article-title":"Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system","volume":"5","author":"Rapin","year":"2010","journal-title":"PLoS ONE"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/14\/2013\/48933124\/bioinformatics_27_14_2013.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/14\/2013\/48933124\/bioinformatics_27_14_2013.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:46:57Z","timestamp":1674823617000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/14\/2013\/195287"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,6,17]]},"references-count":4,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2011,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr335","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2011,7]]},"published":{"date-parts":[[2011,6,17]]}}}