{"id":"https://openalex.org/W2152065574","doi":"https://doi.org/10.1093/bioinformatics/btr335","title":"Immune system simulation online","display_name":"Immune system simulation online","publication_year":2011,"publication_date":"2011-06-17","ids":{"openalex":"https://openalex.org/W2152065574","doi":"https://doi.org/10.1093/bioinformatics/btr335","mag":"2152065574","pmid":"https://pubmed.ncbi.nlm.nih.gov/21685045"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr335","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/14/2013/6142582/btr335.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/14/2013/6142582/btr335.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032007875","display_name":"Nicolas Rapin","orcid":"https://orcid.org/0000-0001-5208-8874"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Nicolas Rapin","raw_affiliation_strings":["Biotech Research & Innovation Centre and Bioinformatics Centre, University of Copenhagen, DK-2200 Copenhagen N, Denmark","Biotech Research & Innovation Centre (BRIC) and Bioinformatics Centre, University of Copenhagen, DK-2200 Copenhagen N,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotech Research & Innovation Centre and Bioinformatics Centre, University of Copenhagen, DK-2200 Copenhagen N, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Biotech Research & Innovation Centre (BRIC) and Bioinformatics Centre, University of Copenhagen, DK-2200 Copenhagen N,","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071462078","display_name":"Ole Lund","orcid":"https://orcid.org/0000-0003-1108-0491"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Ole Lund","raw_affiliation_strings":["Center for Biological Sequence Analysis (CBS), Technical University of Denmark, DK-2800 Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biological Sequence Analysis (CBS), Technical University of Denmark, DK-2800 Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010454141","display_name":"Filippo Castiglione","orcid":"https://orcid.org/0000-0002-1442-3552"},"institutions":[{"id":"https://openalex.org/I4210106125","display_name":"Istituto per le Applicazioni del Calcolo Mauro Picone","ror":"https://ror.org/00ygy3d85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210106125","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Filippo Castiglione","raw_affiliation_strings":["Istituto per le Applicazioni del Calcolo \"M.Picone\" of the National Research Council of Italy, 00185 Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Istituto per le Applicazioni del Calcolo \"M.Picone\" of the National Research Council of Italy, 00185 Rome, Italy","institution_ids":["https://openalex.org/I4210106125","https://openalex.org/I4210155236"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5010454141"],"corresponding_institution_ids":["https://openalex.org/I4210106125","https://openalex.org/I4210155236"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0947,"has_fulltext":true,"cited_by_count":228,"citation_normalized_percentile":{"value":0.76401191,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"27","issue":"14","first_page":"2013","last_page":"2014"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.974399983882904,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.974399983882904,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12391","display_name":"Artificial Immune Systems Applications","score":0.018699999898672104,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6409543752670288},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.631151020526886},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32227015495300293},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21452072262763977},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.20502620935440063}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6409543752670288},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.631151020526886},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32227015495300293},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21452072262763977},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.20502620935440063}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007107","descriptor_name":"Immune System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007107","descriptor_name":"Immune System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007107","descriptor_name":"Immune System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008214","descriptor_name":"Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008214","descriptor_name":"Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008214","descriptor_name":"Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009862","descriptor_name":"Online Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009862","descriptor_name":"Online Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009862","descriptor_name":"Online Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btr335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr335","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/14/2013/6142582/btr335.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21685045","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21685045","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/14/2013","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/14/2013","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/8494849c-978b-47ee-b100-14e3d03a99b4","is_oa":false,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/8494849c-978b-47ee-b100-14e3d03a99b4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Rapin , N P J-P , Lund , O & Castiglione , F 2011 , ' Immune system simulation online ' , Bioinformatics , vol. 27 , no. 14 , pp. 2013-4 . https://doi.org/10.1093/bioinformatics/btr335","raw_type":"article"},{"id":"pmh:oai:pure.atira.dk:publications/69afa387-d9ab-4985-b84f-5e0448790411","is_oa":false,"landing_page_url":"https://orbit.dtu.dk/en/publications/69afa387-d9ab-4985-b84f-5e0448790411","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Rapin , N , Lund , O &amp; Castiglione , F 2011 , ' Immune system simulation online ' , Bioinformatics , vol. 27 , no. 14 , pp. 2013-2014 . https://doi.org/10.1093/bioinformatics/btr335","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr335","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/14/2013/6142582/btr335.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2152065574.pdf","grobid_xml":"https://content.openalex.org/works/W2152065574.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W1982271112","https://openalex.org/W2035240910","https://openalex.org/W2074107830","https://openalex.org/W2171546617"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,66],"recognition":[2,67],"of":[3,10,18,40,51,55,111],"antigenic":[4,57],"peptides":[5,62],"is":[6],"a":[7,29,112,128],"major":[8],"event":[9],"an":[11,37],"immune":[12,20,42],"response.":[13],"In":[14],"current":[15],"mesoscopic-scale":[16],"simulators":[17],"the":[19,41,49,52,56,108,125],"system,":[21],"this":[22],"crucial":[23],"step":[24],"has":[25],"been":[26],"modeled":[27],"in":[28,127],"very":[30],"approximated":[31],"way.":[32],"RESULTS:":[33],"We":[34],"have":[35],"equipped":[36],"agent-based":[38],"model":[39],"system":[43],"with":[44],"immuno-informatics":[45],"methods":[46],"to":[47,63,103],"allow":[48],"simulation":[50],"cardinal":[53],"events":[54],"recognition,":[58],"going":[59],"from":[60,94],"single":[61],"whole":[64],"proteomes.":[65],"process":[68],"accounts":[69],"for":[70,120],"B":[71],"cell-epitopes":[72],"prediction":[73,84,98],"through":[74,87],"Parker-scale":[75],"affinity":[76],"estimation,":[77],"class":[78],"I":[79],"and":[80,85,100],"II":[81],"HLA":[82,96],"peptide":[83],"binding":[86,102],"position-specific":[88],"scoring":[89],"matrices":[90],"based":[91],"on":[92],"information":[93],"known":[95],"epitopes":[97],"tools,":[99],"TCR":[101],"HLA-peptide":[104],"complex":[105],"calculated":[106],"as":[107],"averaged":[109],"sum":[110],"residue-residue":[113],"contact":[114],"potential.":[115],"These":[116],"steps":[117],"are":[118],"executed":[119],"all":[121],"lymphocytes":[122],"agents":[123],"encountering":[124],"antigen":[126],"wide-reaching":[129],"Monte":[130],"Carlo":[131],"simulation.":[132],"AVAILABILITY:":[133],"http://www.cbs.dtu.dk/services/C-ImmSim-10.1/":[134]},"counts_by_year":[{"year":2026,"cited_by_count":38},{"year":2025,"cited_by_count":67},{"year":2024,"cited_by_count":40},{"year":2023,"cited_by_count":25},{"year":2022,"cited_by_count":26},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2025-10-10T00:00:00"}
