{"id":"https://openalex.org/W2125644345","doi":"https://doi.org/10.1371/journal.pcbi.1000107","title":"Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan","display_name":"Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan","publication_year":2008,"publication_date":"2008-07-03","ids":{"openalex":"https://openalex.org/W2125644345","doi":"https://doi.org/10.1371/journal.pcbi.1000107","mag":"2125644345","pmid":"https://pubmed.ncbi.nlm.nih.gov/18604266"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000107","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000107","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000107&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000107&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076702280","display_name":"Morten Nielsen","orcid":"https://orcid.org/0000-0001-7885-4311"},"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":true,"raw_author_name":"Morten Nielsen","raw_affiliation_strings":["Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark. mniel@cbs.dtu.dk","Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Lyngby Denmark"],"affiliations":[{"raw_affiliation_string":"Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark. mniel@cbs.dtu.dk","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Lyngby Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109211420","display_name":"Claus Lundegaard","orcid":null},"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":"Claus Lundegaard","raw_affiliation_strings":["Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark","Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Lyngby Denmark"],"affiliations":[{"raw_affiliation_string":"Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Lyngby Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028714889","display_name":"Thomas Blicher","orcid":null},"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":"Thomas Blicher","raw_affiliation_strings":["Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark","Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Lyngby Denmark"],"affiliations":[{"raw_affiliation_string":"Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Lyngby Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023547268","display_name":"Bjoern Peters","orcid":"https://orcid.org/0000-0002-8457-6693"},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bjoern Peters","raw_affiliation_strings":["La Jolla Institute for Allergy and Immunology, San Diego, California, United States of America"],"affiliations":[{"raw_affiliation_string":"La Jolla Institute for Allergy and Immunology, San Diego, California, United States of America","institution_ids":["https://openalex.org/I1311191458"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010966529","display_name":"Alessandro Sette","orcid":"https://orcid.org/0000-0001-7013-2250"},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alessandro Sette","raw_affiliation_strings":["La Jolla Institute for Allergy and Immunology, San Diego, California, United States of America"],"affiliations":[{"raw_affiliation_string":"La Jolla Institute for Allergy and Immunology, San Diego, California, United States of America","institution_ids":["https://openalex.org/I1311191458"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070388321","display_name":"Sune Justesen","orcid":"https://orcid.org/0000-0002-3039-2178"},"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":"Sune Justesen","raw_affiliation_strings":["Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Denmark","Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, , Denmark"],"affiliations":[{"raw_affiliation_string":"Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, , Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004800654","display_name":"S\u00f8ren Buus","orcid":"https://orcid.org/0000-0001-8363-1999"},"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":"S\u00f8ren Buus","raw_affiliation_strings":["Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Denmark","Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, , Denmark"],"affiliations":[{"raw_affiliation_string":"Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, , Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"last","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, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark","Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Lyngby Denmark"],"affiliations":[{"raw_affiliation_string":"Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Lyngby Denmark","institution_ids":["https://openalex.org/I96673099"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5076702280"],"corresponding_institution_ids":["https://openalex.org/I96673099"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":9.6814,"has_fulltext":true,"cited_by_count":293,"citation_normalized_percentile":{"value":0.98725413,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"4","issue":"7","first_page":"e1000107","last_page":"e1000107"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":1.0,"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":1.0,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.9983999729156494,"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"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9980000257492065,"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/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.7837815284729004},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.708246648311615},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.578218400478363},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.5346271991729736},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.513366162776947},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.5105634927749634},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.5044218301773071},{"id":"https://openalex.org/keywords/hla-dr","display_name":"HLA-DR","score":0.43102627992630005},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4275122582912445},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.2913914918899536},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21991828083992004},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12480854988098145}],"concepts":[{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.7837815284729004},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.708246648311615},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.578218400478363},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.5346271991729736},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.513366162776947},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5105634927749634},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.5044218301773071},{"id":"https://openalex.org/C2779067128","wikidata":"https://www.wikidata.org/wiki/Q5630163","display_name":"HLA-DR","level":3,"score":0.43102627992630005},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4275122582912445},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.2913914918899536},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21991828083992004},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12480854988098145}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006684","descriptor_name":"HLA-DR Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006684","descriptor_name":"HLA-DR Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006684","descriptor_name":"HLA-DR Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006684","descriptor_name":"HLA-DR Antigens","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006684","descriptor_name":"HLA-DR Antigens","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006684","descriptor_name":"HLA-DR Antigens","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006684","descriptor_name":"HLA-DR Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006684","descriptor_name":"HLA-DR Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006684","descriptor_name":"HLA-DR Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1000107","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000107","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000107&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:18604266","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18604266","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1000107","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000107","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:6a407ec0fd0045ad9623747fb679cebf","is_oa":true,"landing_page_url":"https://doaj.org/article/6a407ec0fd0045ad9623747fb679cebf","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 4, Iss 7, p e1000107 (2008)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/150365","is_oa":true,"landing_page_url":"https://figshare.com/articles/Quantitative_Predictions_of_Peptide_Binding_to_Any_HLA_DR_Molecule_of_Known_Sequence_NetMHCIIpan/150365","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:2430535","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2430535","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/fe8e49a0-ebc7-11dd-bf70-000ea68e967b","is_oa":false,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/fe8e49a0-ebc7-11dd-bf70-000ea68e967b","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":"Nielsen , M , Lundegaard , C , Blicher , T , Peters , B , Sette , A , Justesen , S , Buus , S & Lund , O 2008 , ' Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan ' , PLoS Computational Biology , vol. 4 , no. 7 , pp. e1000107 . https://doi.org/10.1371/journal.pcbi.1000107","raw_type":"article"},{"id":"pmh:oai:pure.atira.dk:publications/9728428a-5882-4c4f-859d-46a156aaecb6","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/9728428a-5882-4c4f-859d-46a156aaecb6","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nielsen , M , Lundegaard , C , Blicher , T , Peters , B , Sette , A , Justesen , S , Buus , S &amp; Lund , O 2008 , ' Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan ' , P L o S Computational Biology (Online) , vol. 4 , no. 7 , pp. e1000107 . https://doi.org/10.1371/journal.pcbi.1000107","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000107","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000107","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000107&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G116422006","display_name":null,"funder_award_id":"HHSN26620040006C","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7752622008","display_name":null,"funder_award_id":"HHSN266200400025C","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2125644345.pdf","grobid_xml":"https://content.openalex.org/works/W2125644345.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1526446612","https://openalex.org/W1596377987","https://openalex.org/W1824426708","https://openalex.org/W1970089737","https://openalex.org/W1982752226","https://openalex.org/W1984685993","https://openalex.org/W1990748933","https://openalex.org/W1991461541","https://openalex.org/W1994048581","https://openalex.org/W1998319032","https://openalex.org/W1999022648","https://openalex.org/W2003934979","https://openalex.org/W2019711015","https://openalex.org/W2025729280","https://openalex.org/W2039585266","https://openalex.org/W2044071382","https://openalex.org/W2045175984","https://openalex.org/W2047544230","https://openalex.org/W2047989143","https://openalex.org/W2050947321","https://openalex.org/W2081400647","https://openalex.org/W2094706980","https://openalex.org/W2097398162","https://openalex.org/W2099500226","https://openalex.org/W2101423456","https://openalex.org/W2103498243","https://openalex.org/W2105699887","https://openalex.org/W2118854505","https://openalex.org/W2125732073","https://openalex.org/W2135455279","https://openalex.org/W2137995988","https://openalex.org/W2142636897","https://openalex.org/W2142739377","https://openalex.org/W2143210482","https://openalex.org/W2144185370","https://openalex.org/W2148853951","https://openalex.org/W2149350146","https://openalex.org/W2160583217","https://openalex.org/W2395173985","https://openalex.org/W2412371732","https://openalex.org/W4231722547","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2021824670","https://openalex.org/W203802859","https://openalex.org/W2381567441","https://openalex.org/W3111171798","https://openalex.org/W1813280497","https://openalex.org/W147742377","https://openalex.org/W2019540705","https://openalex.org/W4296157684","https://openalex.org/W4366742782","https://openalex.org/W3215268238"],"abstract_inverted_index":{"CD4":[0],"positive":[1],"T":[2],"helper":[3],"cells":[4,12],"control":[5],"many":[6],"aspects":[7],"of":[8,25,38,49,55,63,80,87,98,105,140,145,179,217,247,254,268],"specific":[9,14,180],"immunity.":[10],"These":[11],"are":[13],"for":[15,52,77,131,158,173,182,211,294],"peptides":[16,39],"derived":[17,93,147],"from":[18,94],"protein":[19],"antigens":[20],"and":[21,116,126,154,277],"presented":[22,263],"by":[23],"molecules":[24,46,133],"the":[26,106,122,141,167,177,183,194,215,228,248,252,262,266,272,285],"extremely":[27],"polymorphic":[28],"major":[29],"histocompatibility":[30],"complex":[31],"(MHC)":[32],"class":[33,44,67,149,297],"II":[34,45,150,298],"system.":[35],"The":[36,90,163],"identification":[37,144,157],"that":[40,75,166,227,261,278],"bind":[41],"to":[42,83,191,233,250,283],"MHC":[43,66,273,286,296],"is":[47,59,92,137],"therefore":[48],"pivotal":[50],"importance":[51],"rational":[53],"discovery":[54,275],"immune":[56],"epitopes.":[57],"HLA-DR":[58,85,100,111,132,161,174,205,255],"a":[60,64,72,95,289],"prominent":[61],"example":[62],"human":[65],"II.":[68],"Here,":[69],"we":[70],"present":[71],"method,":[73],"NetMHCIIpan,":[74],"allows":[76],"pan-specific":[78],"predictions":[79],"peptide":[81,115,128],"binding":[82,101,129,155,172,299],"any":[84],"molecule":[86,185],"known":[88,110],"sequence.":[89],"method":[91,123,142,168,200,229,249,264],"large":[96],"compilation":[97],"quantitative":[99],"events":[102],"covering":[103],"14":[104],"more":[107],"than":[108],"500":[109],"alleles.":[112,224],"Taking":[113],"both":[114],"HLA":[117,148],"sequence":[118],"information":[119],"into":[120],"account,":[121],"can":[124,169,230,280],"generalize":[125],"predict":[127,171],"also":[130],"where":[134],"experimental":[135],"data":[136,181],"absent.":[138],"Validation":[139],"includes":[143],"endogenously":[146],"ligands,":[151],"cross-validation,":[152],"leave-one-molecule-out,":[153],"motif":[156],"hitherto":[159,236],"uncharacterized":[160,237],"molecules.":[162],"validation":[164],"shows":[165],"successfully":[170],"molecules-even":[175],"in":[176,186,214,244],"absence":[178],"particular":[184],"question.":[187],"Moreover,":[188],"when":[189],"compared":[190],"TEPITOPE,":[192],"currently":[193],"only":[195],"other":[196],"publicly":[197],"available":[198],"prediction":[199],"aiming":[201],"at":[202],"providing":[203],"broad":[204],"allelic":[206],"coverage,":[207],"NetMHCIIpan":[208],"performs":[209],"equivalently":[210],"alleles":[212],"included":[213],"training":[216],"TEPITOPE":[218,221],"while":[219],"outperforming":[220],"on":[222],"novel":[223],"We":[225,258],"propose":[226],"be":[231,241,281],"used":[232,282],"identify":[234],"those":[235],"alleles,":[238],"which":[239],"should":[240],"addressed":[242],"experimentally":[243],"future":[245],"updates":[246],"cover":[251],"polymorphism":[253,274],"most":[256],"efficiently.":[257],"thus":[259],"conclude":[260],"meets":[265],"challenge":[267],"keeping":[269],"up":[270],"with":[271],"rate":[276],"it":[279],"sample":[284],"\"space,\"":[287],"enabling":[288],"highly":[290],"efficient":[291],"iterative":[292],"process":[293],"improving":[295],"predictions.":[300]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":22},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":16},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":18},{"year":2013,"cited_by_count":21},{"year":2012,"cited_by_count":17}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
