{"id":"https://openalex.org/W3114418016","doi":"https://doi.org/10.1093/bioinformatics/btaa1050","title":"High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides","display_name":"High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3114418016","doi":"https://doi.org/10.1093/bioinformatics/btaa1050","mag":"3114418016","pmid":"https://pubmed.ncbi.nlm.nih.gov/33355667"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa1050","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1050","pdf_url":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8016493","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058720973","display_name":"Tyler Borrman","orcid":"https://orcid.org/0000-0001-7386-8159"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tyler Borrman","raw_affiliation_strings":["Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School , Worcester, MA 01605, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School , Worcester, MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046287489","display_name":"Brian G. Pierce","orcid":"https://orcid.org/0000-0003-4821-0368"},"institutions":[{"id":"https://openalex.org/I4210152530","display_name":"Advanced Bioscience Laboratories (United States)","ror":"https://ror.org/04v1j8c44","country_code":"US","type":"company","lineage":["https://openalex.org/I4210152530"]},{"id":"https://openalex.org/I4389425230","display_name":"Institute for Bioscience and Biotechnology Research","ror":"https://ror.org/02zs3hb12","country_code":null,"type":"facility","lineage":["https://openalex.org/I126744593","https://openalex.org/I1321296531","https://openalex.org/I1343035065","https://openalex.org/I4389425230","https://openalex.org/I66946132"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian G Pierce","raw_affiliation_strings":["Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD 20742, USA","University of Maryland Institute for Bioscience and Biotechnology Research , Rockville, MD 20850, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD 20742, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"University of Maryland Institute for Bioscience and Biotechnology Research , Rockville, MD 20850, USA","institution_ids":["https://openalex.org/I4210152530","https://openalex.org/I4389425230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065844672","display_name":"Thom Vreven","orcid":"https://orcid.org/0000-0003-3413-806X"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thom Vreven","raw_affiliation_strings":["Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School , Worcester, MA 01605, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School , Worcester, MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082462618","display_name":"Brian M. Baker","orcid":"https://orcid.org/0000-0002-0864-0964"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian M Baker","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, IN 46556, USA","Harper Cancer Research Institute, University of Notre Dame , Notre Dame, IN 46556, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, IN 46556, USA","institution_ids":["https://openalex.org/I107639228"]},{"raw_affiliation_string":"Harper Cancer Research Institute, University of Notre Dame , Notre Dame, IN 46556, USA","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084369008","display_name":"Zhiping Weng","orcid":"https://orcid.org/0000-0002-3032-7966"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhiping Weng","raw_affiliation_strings":["Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School , Worcester, MA 01605, USA"],"raw_orcid":"https://orcid.org/0000-0002-3032-7966","affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School , Worcester, MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5084369008"],"corresponding_institution_ids":["https://openalex.org/I166722992"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1391,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.77782894,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"36","issue":"22-23","first_page":"5377","last_page":"5385"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.6909000277519226,"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":0.6909000277519226,"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":0.26170000433921814,"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/T11171","display_name":"Diabetes and associated disorders","score":0.006899999920278788,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.8613981604576111},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6895936727523804},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5868225693702698},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.5205063223838806},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5164259076118469},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.4753815233707428},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.4513876736164093},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.3876649737358093},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3263276219367981},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.30294322967529297},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1727237105369568},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13049596548080444}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.8613981604576111},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6895936727523804},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5868225693702698},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.5205063223838806},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5164259076118469},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.4753815233707428},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.4513876736164093},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.3876649737358093},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3263276219367981},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.30294322967529297},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1727237105369568},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13049596548080444}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa1050","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1050","pdf_url":null,"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:33355667","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33355667","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:escholarship.umassmed.edu:faculty_pubs-2901","is_oa":false,"landing_page_url":"https://escholarship.umassmed.edu/faculty_pubs/1881","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"University of Massachusetts Medical School Faculty Publications","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8016493","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8016493","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8016493","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8016493","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[{"score":0.47999998927116394,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G155194203","display_name":null,"funder_award_id":"R01 GM116960","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2653397923","display_name":null,"funder_award_id":"R01GM103773","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5302408348","display_name":null,"funder_award_id":"R01GM116960","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5926090212","display_name":null,"funder_award_id":"R01 GM126299","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6229892521","display_name":null,"funder_award_id":"R35 GM118166","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8466817904","display_name":null,"funder_award_id":"R35GM118166","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8467143682","display_name":null,"funder_award_id":"R01GM126299","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G97899014","display_name":null,"funder_award_id":"R01 GM103773","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W1481073656","https://openalex.org/W1940355479","https://openalex.org/W1951588750","https://openalex.org/W1973980688","https://openalex.org/W1974782594","https://openalex.org/W1979731533","https://openalex.org/W1982715221","https://openalex.org/W1986216579","https://openalex.org/W1991772842","https://openalex.org/W1993446370","https://openalex.org/W2008557466","https://openalex.org/W2020312840","https://openalex.org/W2021310372","https://openalex.org/W2021507425","https://openalex.org/W2032428654","https://openalex.org/W2049204549","https://openalex.org/W2057687465","https://openalex.org/W2068872497","https://openalex.org/W2070748533","https://openalex.org/W2072784497","https://openalex.org/W2078866994","https://openalex.org/W2084612387","https://openalex.org/W2091567124","https://openalex.org/W2106582884","https://openalex.org/W2113773464","https://openalex.org/W2114559206","https://openalex.org/W2117333383","https://openalex.org/W2121261324","https://openalex.org/W2143210482","https://openalex.org/W2145126338","https://openalex.org/W2146652028","https://openalex.org/W2157384708","https://openalex.org/W2158682956","https://openalex.org/W2169026862","https://openalex.org/W2201713963","https://openalex.org/W2271914738","https://openalex.org/W2507608410","https://openalex.org/W2573505039","https://openalex.org/W2584679456","https://openalex.org/W2743893844","https://openalex.org/W2744957082","https://openalex.org/W2759890769","https://openalex.org/W2769985437","https://openalex.org/W2775848633","https://openalex.org/W2778215749","https://openalex.org/W2889980427","https://openalex.org/W2900127803","https://openalex.org/W2900711722","https://openalex.org/W2901423492","https://openalex.org/W2904572271","https://openalex.org/W2910869058","https://openalex.org/W2938592129","https://openalex.org/W2950352272","https://openalex.org/W2953065444","https://openalex.org/W2968781851","https://openalex.org/W2968803773","https://openalex.org/W2968849363","https://openalex.org/W2972612455","https://openalex.org/W4242761032","https://openalex.org/W6662827422","https://openalex.org/W6824513471"],"related_works":["https://openalex.org/W2011835836","https://openalex.org/W2089872551","https://openalex.org/W1973836350","https://openalex.org/W2136036540","https://openalex.org/W2038509173","https://openalex.org/W2075125040","https://openalex.org/W2113488569","https://openalex.org/W3032468696","https://openalex.org/W2176905394","https://openalex.org/W2160899489"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"binding":[2,112,170],"of":[3,48,70,78,87,106,113],"T-cell":[4],"receptors":[5],"(TCRs)":[6],"to":[7,60,65,109],"their":[8,159],"target":[9],"peptide":[10],"MHC":[11],"(pMHC)":[12],"ligands":[13],"initializes":[14],"the":[15,26,49,74,85,103,111,168],"cell-mediated":[16],"immune":[17,36],"response.":[18],"In":[19],"autoimmune":[20,71],"diseases":[21],"such":[22,62],"as":[23,31],"multiple":[24,130],"sclerosis,":[25],"TCR":[27,51,124],"erroneously":[28],"recognizes":[29],"self-peptides":[30],"foreign":[32,53,79],"and":[33,98,121,191],"activates":[34],"an":[35,82,94],"response":[37],"against":[38],"healthy":[39],"cells.":[40],"Such":[41],"responses":[42],"can":[43],"be":[44,58],"triggered":[45],"by":[46],"cross-recognition":[47],"autoreactive":[50],"with":[52,129,144],"peptides.":[54,89,115,181],"Hence,":[55],"it":[56],"would":[57],"desirable":[59],"identify":[61],"foreign-antigen":[63],"triggers":[64],"provide":[66],"a":[67,127,148,177],"mechanistic":[68],"understanding":[69],"diseases.":[72],"However,":[73],"large":[75],"sequence":[76],"space":[77],"antigens":[80],"presents":[81],"obstacle":[83],"in":[84,95,158],"identification":[86],"cross-reactive":[88,114],"RESULTS:":[90],"Here,":[91],"we":[92],"present":[93],"silico":[96],"modeling":[97],"scoring":[99],"method":[100,165],"which":[101],"exploits":[102],"structural":[104],"properties":[105],"TCR-pMHC":[107,161],"complexes":[108],"predict":[110],"We":[116],"analyzed":[117],"three":[118],"mouse":[119],"TCRs":[120,136],"one":[122],"human":[123],"isolated":[125],"from":[126,172],"patient":[128],"sclerosis.":[131],"Cross-reactive":[132],"peptides":[133,157,171],"for":[134,151],"these":[135],"were":[137,186],"previously":[138],"identified":[139],"via":[140],"yeast":[141],"display":[142],"coupled":[143],"deep":[145],"sequencing,":[146],"providing":[147],"robust":[149],"dataset":[150],"evaluating":[152],"our":[153,164],"method.":[154],"Modeling":[155],"query":[156],"associated":[160],"crystal":[162],"structures,":[163],"accurately":[166],"selected":[167],"top":[169],"sets":[173],"containing":[174],"more":[175],"than":[176],"hundred":[178],"thousand":[179],"unique":[180],"AVAILABILITY":[182],"AND":[183],"IMPLEMENTATION:":[184],"Analyses":[185],"performed":[187],"using":[188],"custom":[189],"Python":[190],"R":[192],"scripts":[193],"available":[194,202],"at":[195,203],"https://github.com/weng-lab/antigen-predict.":[196],"SUPPLEMENTARY":[197],"INFORMATION:":[198],"Supplementary":[199],"data":[200],"are":[201],"Bioinformatics":[204],"online.":[205]},"counts_by_year":[{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
