{"id":"https://openalex.org/W3011040738","doi":"https://doi.org/10.1093/bioinformatics/btaa194","title":"TCRBuilder: multi-state T-cell receptor structure prediction","display_name":"TCRBuilder: multi-state T-cell receptor structure prediction","publication_year":2020,"publication_date":"2020-03-13","ids":{"openalex":"https://openalex.org/W3011040738","doi":"https://doi.org/10.1093/bioinformatics/btaa194","mag":"3011040738","pmid":"https://pubmed.ncbi.nlm.nih.gov/32181809"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa194","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa194","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062359376","display_name":"Wing Ki Wong","orcid":"https://orcid.org/0000-0003-4029-6902"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Wing Ki Wong","raw_affiliation_strings":["Department of Statistics , University of Oxford, Oxford OX1 3LB, UK"],"raw_orcid":"https://orcid.org/0000-0003-4029-6902","affiliations":[{"raw_affiliation_string":"Department of Statistics , University of Oxford, Oxford OX1 3LB, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006452408","display_name":"Claire Marks","orcid":"https://orcid.org/0000-0001-5931-2437"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Claire Marks","raw_affiliation_strings":["Department of Statistics , University of Oxford, Oxford OX1 3LB, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics , University of Oxford, Oxford OX1 3LB, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054519833","display_name":"Jinwoo Leem","orcid":"https://orcid.org/0000-0002-7817-3644"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jinwoo Leem","raw_affiliation_strings":["Department of Statistics , University of Oxford, Oxford OX1 3LB, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics , University of Oxford, Oxford OX1 3LB, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102307227","display_name":"Alan P. Lewis","orcid":null},"institutions":[{"id":"https://openalex.org/I188950975","display_name":"GlaxoSmithKline (United Kingdom)","ror":"https://ror.org/01xsqw823","country_code":"GB","type":"company","lineage":["https://openalex.org/I188950975"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alan P Lewis","raw_affiliation_strings":["Data and Computational Sciences , GlaxoSmithKline Research and Development, Stevenage SG1 2NY, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Data and Computational Sciences , GlaxoSmithKline Research and Development, Stevenage SG1 2NY, UK","institution_ids":["https://openalex.org/I188950975"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078567532","display_name":"Jiye Shi","orcid":"https://orcid.org/0000-0002-9628-8680"},"institutions":[{"id":"https://openalex.org/I4210134054","display_name":"UCB Pharma (United Kingdom)","ror":"https://ror.org/03428qp74","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210134054","https://openalex.org/I85722119"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jiye Shi","raw_affiliation_strings":["Department of Chemistry , UCB Pharma, Slough SL1 3WE, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry , UCB Pharma, Slough SL1 3WE, UK","institution_ids":["https://openalex.org/I4210134054"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015572211","display_name":"Charlotte M. Deane","orcid":"https://orcid.org/0000-0003-1388-2252"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Charlotte M Deane","raw_affiliation_strings":["Department of Statistics , University of Oxford, Oxford OX1 3LB, UK"],"raw_orcid":"https://orcid.org/0000-0003-1388-2252","affiliations":[{"raw_affiliation_string":"Department of Statistics , University of Oxford, Oxford OX1 3LB, UK","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5015572211"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8934,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.72509385,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"36","issue":"11","first_page":"3580","last_page":"3581"},"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":0.8083999752998352,"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":0.8083999752998352,"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":0.08860000222921371,"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":0.02759999968111515,"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":0.9204928874969482},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.7210173010826111},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6573730707168579},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4380251467227936},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4345555007457733},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.43452876806259155},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43298986554145813},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.39436793327331543},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.35879260301589966},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.27783945202827454},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.2146221399307251},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15895766019821167}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.9204928874969482},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.7210173010826111},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6573730707168579},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4380251467227936},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4345555007457733},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.43452876806259155},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43298986554145813},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.39436793327331543},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.35879260301589966},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.27783945202827454},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.2146221399307251},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15895766019821167}],"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":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa194","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa194","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:32181809","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32181809","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:ora.ox.ac.uk:uuid:3edc2615-ad22-4be6-abf4-c7e68bed3ec4","is_oa":false,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:3edc2615-ad22-4be6-abf4-c7e68bed3ec4","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Symplectic Elements","raw_type":"Journal article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.46000000834465027}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1481701911","https://openalex.org/W2000779612","https://openalex.org/W2017956110","https://openalex.org/W2073392655","https://openalex.org/W2146074801","https://openalex.org/W2150345297","https://openalex.org/W2474661075","https://openalex.org/W2574510864","https://openalex.org/W2766169371","https://openalex.org/W2803170063","https://openalex.org/W2951119766","https://openalex.org/W2981124539"],"related_works":["https://openalex.org/W2011835836","https://openalex.org/W2089872551","https://openalex.org/W1973836350","https://openalex.org/W2038509173","https://openalex.org/W2136036540","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],"T-cell":[1],"receptors":[2],"(TCRs)":[3],"are":[4,127],"immune":[5],"proteins":[6],"that":[7],"primarily":[8],"target":[9],"peptide":[10],"antigens":[11],"presented":[12],"by":[13],"the":[14,52,93,97,102],"major":[15],"histocompatibility":[16],"complex.":[17],"They":[18],"tend":[19],"to":[20,37,63],"have":[21,34],"lower":[22],"specificity":[23],"and":[24,30],"affinity":[25],"than":[26],"their":[27,31,48],"antibody":[28],"counterparts,":[29],"binding":[32,98],"sites":[33],"been":[35],"shown":[36],"adopt":[38],"multiple":[39],"conformations,":[40],"which":[41,59,110],"is":[42,111],"potentially":[43],"an":[44,88],"important":[45],"factor":[46],"for":[47],"polyspecificity.":[49],"None":[50],"of":[51,90,96,104],"current":[53],"TCR-modelling":[54],"tools":[55],"predict":[56,65],"this":[57],"variability":[58],"limits":[60],"our":[61],"ability":[62],"accurately":[64],"TCR":[66,74],"binding.":[67],"RESULTS:":[68],"We":[69],"present":[70],"TCRBuilder,":[71],"a":[72,79,85],"multi-state":[73],"structure":[75],"prediction":[76],"tool.":[77],"Given":[78],"paired":[80],"\u03b1\u03b2TCR":[81],"sequence,":[82],"TCRBuilder":[83],"returns":[84],"model":[86],"or":[87],"ensemble":[89],"models":[91],"covering":[92],"potential":[94],"conformations":[95],"site.":[99],"This":[100],"enables":[101],"analysis":[103],"structurally":[105],"driven":[106],"polyspecificity":[107],"in":[108],"TCRs,":[109],"not":[112],"possible":[113],"with":[114],"existing":[115],"tools.":[116],"AVAILABILITY":[117],"AND":[118],"IMPLEMENTATION:":[119],"http://opig.stats.ox.ac.uk/resources.":[120],"CONTACT:":[121],"deane@stats.ox.ac.uk.":[122],"SUPPLEMENTARY":[123],"INFORMATION:":[124],"Supplementary":[125],"data":[126],"available":[128],"at":[129],"Bioinformatics":[130],"online.":[131]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
