{"id":"https://openalex.org/W2955439997","doi":"https://doi.org/10.1093/bioinformatics/btz517","title":"TCR3d: The T cell receptor structural repertoire database","display_name":"TCR3d: The T cell receptor structural repertoire database","publication_year":2019,"publication_date":"2019-06-21","ids":{"openalex":"https://openalex.org/W2955439997","doi":"https://doi.org/10.1093/bioinformatics/btz517","mag":"2955439997","pmid":"https://pubmed.ncbi.nlm.nih.gov/31240309"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz517","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5323/31797988/btz517.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5323/31797988/btz517.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084358881","display_name":"Ragul Gowthaman","orcid":"https://orcid.org/0000-0002-0008-6401"},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]},{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]},{"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/I4390039317","display_name":"University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center","ror":"https://ror.org/01vft3j45","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I14285509","https://openalex.org/I4390039317"]},{"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":"Ragul Gowthaman","raw_affiliation_strings":["Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD, USA","University of Maryland Institute for Bioscience and Biotechnology Research , Rockville, MD, USA","University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center , Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"University of Maryland Institute for Bioscience and Biotechnology Research , Rockville, MD, USA","institution_ids":["https://openalex.org/I126744593","https://openalex.org/I1321296531","https://openalex.org/I66946132","https://openalex.org/I4389425230"]},{"raw_affiliation_string":"University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center , Baltimore, MD, USA","institution_ids":["https://openalex.org/I126744593","https://openalex.org/I4390039317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046287489","display_name":"Brian G. Pierce","orcid":"https://orcid.org/0000-0003-4821-0368"},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]},{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]},{"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/I4390039317","display_name":"University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center","ror":"https://ror.org/01vft3j45","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I14285509","https://openalex.org/I4390039317"]},{"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":true,"raw_author_name":"Brian G Pierce","raw_affiliation_strings":["Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD, USA","University of Maryland Institute for Bioscience and Biotechnology Research , Rockville, MD, USA","University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center , Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"University of Maryland Institute for Bioscience and Biotechnology Research , Rockville, MD, USA","institution_ids":["https://openalex.org/I126744593","https://openalex.org/I1321296531","https://openalex.org/I66946132","https://openalex.org/I4389425230"]},{"raw_affiliation_string":"University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center , Baltimore, MD, USA","institution_ids":["https://openalex.org/I126744593","https://openalex.org/I4390039317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5046287489"],"corresponding_institution_ids":["https://openalex.org/I126744593","https://openalex.org/I1321296531","https://openalex.org/I4389425230","https://openalex.org/I4390039317","https://openalex.org/I66946132"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.7624,"has_fulltext":true,"cited_by_count":124,"citation_normalized_percentile":{"value":0.94245816,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"35","issue":"24","first_page":"5323","last_page":"5325"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.7102000117301941,"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"}},"topics":[{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.7102000117301941,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.043699998408555984,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.030700000002980232,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.8858246803283691},{"id":"https://openalex.org/keywords/repertoire","display_name":"Repertoire","score":0.6234227418899536},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6041017770767212},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.5371826887130737},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5107734203338623},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4939747452735901},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43732500076293945},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.37204277515411377},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.3047369122505188},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20733174681663513}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.8858246803283691},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.6234227418899536},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6041017770767212},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.5371826887130737},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5107734203338623},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4939747452735901},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43732500076293945},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.37204277515411377},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.3047369122505188},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20733174681663513},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000941","descriptor_name":"Antigens","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000941","descriptor_name":"Antigens","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000941","descriptor_name":"Antigens","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz517","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5323/31797988/btz517.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31240309","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31240309","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:europepmc.org:5915396","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6954642","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz517","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5323/31797988/btz517.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.4000000059604645,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G8281964143","display_name":null,"funder_award_id":"GM126299","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/W2955439997.pdf","grobid_xml":"https://content.openalex.org/works/W2955439997.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1978499958","https://openalex.org/W2021310372","https://openalex.org/W2120518061","https://openalex.org/W2142678478","https://openalex.org/W2146074801","https://openalex.org/W2153105219","https://openalex.org/W2275997631","https://openalex.org/W2467278060","https://openalex.org/W2584679456","https://openalex.org/W2613978126","https://openalex.org/W2670890989","https://openalex.org/W2752126733","https://openalex.org/W2766169371","https://openalex.org/W2803170063","https://openalex.org/W2951959160"],"related_works":["https://openalex.org/W2060496539","https://openalex.org/W4280506224","https://openalex.org/W2018330851","https://openalex.org/W2143290387","https://openalex.org/W3201606428","https://openalex.org/W2040128205","https://openalex.org/W2060075608","https://openalex.org/W2026444950","https://openalex.org/W2092033815","https://openalex.org/W2168929838"],"abstract_inverted_index":{"SUMMARY:":[0],"T":[1,174],"cell":[2,175],"receptors":[3,176],"(TCRs)":[4],"are":[5],"critical":[6],"molecules":[7],"of":[8,14,30,38,41,56,87,138,149],"the":[9,33,96,165],"adaptive":[10],"immune":[11],"system,":[12],"capable":[13],"recognizing":[15],"diverse":[16,54],"antigens,":[17],"including":[18],"peptides,":[19],"lipids":[20],"and":[21,24,35,53,67,75,84,125,143,145,162,177],"small":[22],"molecules,":[23],"represent":[25],"a":[26,44,51,70,99,107,159,168],"rapidly":[27],"growing":[28],"class":[29],"therapeutics.":[31],"Determining":[32],"structural":[34],"mechanistic":[36,85],"basis":[37,86],"TCR":[39,65,88,104,133,152],"targeting":[40],"antigens":[42],"is":[43,156,186],"major":[45],"challenge,":[46],"as":[47,167],"each":[48],"individual":[49],"has":[50],"vast":[52],"repertoire":[55],"TCRs.":[57],"Despite":[58],"shared":[59],"general":[60],"recognition":[61,68],"modes,":[62],"diversity":[63],"in":[64],"sequence":[66],"represents":[69],"challenge":[71],"to":[72,80],"predictive":[73],"modeling":[74],"computational":[76],"techniques":[77],"being":[78],"developed":[79,95],"predict":[81],"antigen":[82,111,118],"specificity":[83],"targeting.":[89],"To":[90],"this":[91],"end,":[92],"we":[93],"have":[94],"TCR3d":[97,113,184],"database,":[98],"resource":[100,170],"containing":[101],"all":[102],"known":[103,141],"structures,":[105,135],"with":[106],"particular":[108],"focus":[109],"on":[110,117,158],"recognition.":[112,179],"provides":[114],"key":[115],"information":[116],"binding":[119],"mode,":[120],"interface":[121],"features,":[122],"loop":[123],"sequences":[124,137],"germline":[126],"gene":[127],"usage.":[128],"Users":[129],"can":[130,163],"interactively":[131],"view":[132],"complex":[134],"search":[136],"interest":[139],"against":[140],"structures":[142],"sequences,":[144],"download":[146],"curated":[147],"datasets":[148],"structurally":[150],"characterized":[151],"complexes.":[153],"This":[154],"database":[155,185],"updated":[157],"weekly":[160],"basis,":[161],"serve":[164],"community":[166],"centralized":[169],"for":[171],"those":[172],"studying":[173],"their":[178],"AVAILABILITY":[180],"AND":[181],"IMPLEMENTATION:":[182],"The":[183],"available":[187],"at":[188],"https://tcr3d.ibbr.umd.edu/.":[189]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":31},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":2}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}
