{"id":"https://openalex.org/W4402977945","doi":"https://doi.org/10.1371/journal.pcbi.1012489","title":"Exploring the potential of structure-based deep learning approaches for T cell receptor design","display_name":"Exploring the potential of structure-based deep learning approaches for T cell receptor design","publication_year":2024,"publication_date":"2024-09-30","ids":{"openalex":"https://openalex.org/W4402977945","doi":"https://doi.org/10.1371/journal.pcbi.1012489","pmid":"https://pubmed.ncbi.nlm.nih.gov/39348412"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012489","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012489","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1012489","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051059732","display_name":"Helder Veras Ribeiro Filho","orcid":"https://orcid.org/0000-0001-8471-207X"},"institutions":[{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Helder V. Ribeiro-Filho","raw_affiliation_strings":["Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, S\u00e3o Paulo, Brazil"],"raw_orcid":"https://orcid.org/0000-0001-8471-207X","affiliations":[{"raw_affiliation_string":"Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060155336","display_name":"Gabriel Ernesto Jara","orcid":"https://orcid.org/0000-0002-5831-1392"},"institutions":[{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Gabriel E. Jara","raw_affiliation_strings":["Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, S\u00e3o Paulo, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-5831-1392","affiliations":[{"raw_affiliation_string":"Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048144057","display_name":"Jo\u00e3o Victor da Silva Guerra","orcid":"https://orcid.org/0000-0002-6800-4425"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]},{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o V. S. Guerra","raw_affiliation_strings":["Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, S\u00e3o Paulo, Brazil","Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, S\u00e3o Paulo, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-6800-4425","affiliations":[{"raw_affiliation_string":"Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]},{"raw_affiliation_string":"Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I181391015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005166629","display_name":"Melyssa Cheung","orcid":"https://orcid.org/0000-0002-3232-2034"},"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":"Melyssa Cheung","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America","Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3232-2034","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America","institution_ids":["https://openalex.org/I4210152530","https://openalex.org/I4389425230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057541000","display_name":"Nathaniel Felbinger","orcid":"https://orcid.org/0009-0009-6956-8888"},"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":"Nathaniel R. Felbinger","raw_affiliation_strings":["Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America","Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America","institution_ids":["https://openalex.org/I4210152530","https://openalex.org/I4389425230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034320215","display_name":"Jos\u00e9 Geraldo de Carvalho Pereira","orcid":"https://orcid.org/0000-0003-1041-0209"},"institutions":[{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 G. C. Pereira","raw_affiliation_strings":["Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, S\u00e3o Paulo, Brazil"],"raw_orcid":"https://orcid.org/0000-0003-1041-0209","affiliations":[{"raw_affiliation_string":"Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]}]},{"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, Maryland, United States of America","Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-4821-0368","affiliations":[{"raw_affiliation_string":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America","institution_ids":["https://openalex.org/I4210152530","https://openalex.org/I4389425230"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065692802","display_name":"Paulo S\u00e9rgio Lopes de Oliveira","orcid":"https://orcid.org/0000-0002-1287-8019"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]},{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Paulo S. Lopes-de-Oliveira","raw_affiliation_strings":["Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, S\u00e3o Paulo, Brazil","Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, S\u00e3o Paulo, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-1287-8019","affiliations":[{"raw_affiliation_string":"Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]},{"raw_affiliation_string":"Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I181391015"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.6123,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.68295561,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"20","issue":"9","first_page":"e1012489","last_page":"e1012489"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9983000159263611,"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":0.9983000159263611,"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/T11491","display_name":"CAR-T cell therapy research","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9922999739646912,"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/computational-biology","display_name":"Computational biology","score":0.6515969634056091},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.6381103992462158},{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.6159957647323608},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"Protein engineering","score":0.533096969127655},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.5092848539352417},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5051186680793762},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.47461003065109253},{"id":"https://openalex.org/keywords/molecular-recognition","display_name":"Molecular recognition","score":0.41543954610824585},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40052059292793274},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.385850727558136},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.3322935104370117},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.33139777183532715},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.24638262391090393},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.2391815185546875},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1767323613166809},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.12448161840438843},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12387073040008545}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6515969634056091},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.6381103992462158},{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.6159957647323608},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.533096969127655},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.5092848539352417},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5051186680793762},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.47461003065109253},{"id":"https://openalex.org/C179303850","wikidata":"https://www.wikidata.org/wiki/Q4300362","display_name":"Molecular recognition","level":3,"score":0.41543954610824585},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40052059292793274},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.385850727558136},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.3322935104370117},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.33139777183532715},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.24638262391090393},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.2391815185546875},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1767323613166809},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.12448161840438843},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12387073040008545},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1371/journal.pcbi.1012489","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012489","pdf_url":null,"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:39348412","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39348412","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:pubmedcentral.nih.gov:11466415","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11466415","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11466415/pdf/pcbi.1012489.pdf","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":"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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012489","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012489","pdf_url":null,"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":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.5}],"awards":[{"id":"https://openalex.org/G2485832188","display_name":null,"funder_award_id":"2022/04260-6","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G2823776494","display_name":null,"funder_award_id":"88887","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"},{"id":"https://openalex.org/G6191138830","display_name":null,"funder_award_id":"88887","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G7189242771","display_name":null,"funder_award_id":"GM144083","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7272414779","display_name":null,"funder_award_id":"88887.928702/2023-00","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"}],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320327334","display_name":"Centro Nacional de Pesquisa em Energia e Materiais","ror":"https://ror.org/05m235j20"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320335750","display_name":"Laborat\u00f3rio Nacional de Bioci\u00eancias","ror":"https://ror.org/04kjcjc51"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":66,"referenced_works":["https://openalex.org/W1855237549","https://openalex.org/W1968984443","https://openalex.org/W1976499671","https://openalex.org/W1994941561","https://openalex.org/W2000702472","https://openalex.org/W2020312840","https://openalex.org/W2026751760","https://openalex.org/W2035266068","https://openalex.org/W2047399603","https://openalex.org/W2053669000","https://openalex.org/W2055043387","https://openalex.org/W2063184115","https://openalex.org/W2072149435","https://openalex.org/W2097356092","https://openalex.org/W2106582884","https://openalex.org/W2114239896","https://openalex.org/W2114850508","https://openalex.org/W2131185370","https://openalex.org/W2143626441","https://openalex.org/W2154319440","https://openalex.org/W2159772201","https://openalex.org/W2166213184","https://openalex.org/W2313116527","https://openalex.org/W2330799739","https://openalex.org/W2404280981","https://openalex.org/W2508425869","https://openalex.org/W2520085530","https://openalex.org/W2584679456","https://openalex.org/W2737196618","https://openalex.org/W2752126733","https://openalex.org/W2759890769","https://openalex.org/W2767331838","https://openalex.org/W2790952361","https://openalex.org/W2900711722","https://openalex.org/W2901331779","https://openalex.org/W2904572271","https://openalex.org/W2910890866","https://openalex.org/W2950612260","https://openalex.org/W2955439997","https://openalex.org/W2966041852","https://openalex.org/W2972102845","https://openalex.org/W3094560178","https://openalex.org/W3109508638","https://openalex.org/W3202105508","https://openalex.org/W4206693359","https://openalex.org/W4207079440","https://openalex.org/W4214927528","https://openalex.org/W4220725839","https://openalex.org/W4220974185","https://openalex.org/W4223581484","https://openalex.org/W4294542662","https://openalex.org/W4296032638","https://openalex.org/W4307166771","https://openalex.org/W4309485183","https://openalex.org/W4313893438","https://openalex.org/W4320896665","https://openalex.org/W4327550249","https://openalex.org/W4352994754","https://openalex.org/W4362579800","https://openalex.org/W4368357399","https://openalex.org/W4383957026","https://openalex.org/W4387440676","https://openalex.org/W4389167075","https://openalex.org/W4399385008","https://openalex.org/W4400985732","https://openalex.org/W6802033083"],"related_works":["https://openalex.org/W2116266427","https://openalex.org/W2991041010","https://openalex.org/W2003675367","https://openalex.org/W2991203454","https://openalex.org/W2512252615","https://openalex.org/W2409023191","https://openalex.org/W3215076145","https://openalex.org/W2005982196","https://openalex.org/W1534529517","https://openalex.org/W4390745893"],"abstract_inverted_index":{"Deep":[0],"learning":[1,157],"methods,":[2,126,160],"trained":[3],"on":[4],"the":[5,18,28,34,50,73,81,101,115,130,151,175,196],"increasing":[6],"set":[7,189],"of":[8,30,36,53,75,84,103,118,134,153,190,198],"available":[9],"protein":[10,19,59,158],"3D":[11],"structures":[12],"and":[13,21,141,162,192,208],"sequences,":[14],"have":[15,26],"substantially":[16],"impacted":[17],"modeling":[20],"design":[22,74,117,159,179,206],"field.":[23],"These":[24],"advancements":[25],"facilitated":[27],"creation":[29],"novel":[31],"proteins,":[32],"or":[33,96],"optimization":[35],"existing":[37],"ones":[38],"designed":[39],"for":[40,123,168,211],"specific":[41],"functions,":[42],"such":[43,54,137],"as":[44,138],"binding":[45,169],"a":[46,187],"target":[47,98,170],"protein.":[48],"Despite":[49],"demonstrated":[51],"potential":[52,152],"approaches":[55],"in":[56,63,87,109,146,164,201],"designing":[57,64,165],"general":[58],"binders,":[60],"their":[61],"application":[62,71],"immunotherapeutics":[65],"remains":[66],"relatively":[67],"underexplored.":[68],"A":[69],"relevant":[70],"is":[72],"T":[76,85],"cell":[77],"receptors":[78],"(TCRs).":[79],"Given":[80],"crucial":[82],"role":[83],"cells":[86,93,99],"mediating":[88],"immune":[89],"responses,":[90],"redirecting":[91],"these":[92,135,199],"to":[94,129,203],"tumor":[95],"infected":[97],"through":[100,177],"engineering":[102],"TCRs":[104,167],"has":[105],"shown":[106],"promising":[107],"results":[108],"treating":[110],"diseases,":[111],"especially":[112],"cancer.":[113],"However,":[114],"computational":[116],"TCR":[119,183],"interactions":[120],"presents":[121],"challenges":[122],"current":[124],"physics-based":[125,205],"particularly":[127],"due":[128],"unique":[131],"natural":[132],"characteristics":[133],"interfaces,":[136],"low":[139],"affinity":[140],"cross-reactivity.":[142],"For":[143],"this":[144,147],"reason,":[145],"study,":[148],"we":[149,185],"explored":[150],"two":[154],"structure-based":[155,193],"deep":[156],"ProteinMPNN":[161],"ESM-IF1,":[163],"fixed-backbone":[166],"antigenic":[171],"peptides":[172],"presented":[173],"by":[174],"MHC":[176],"different":[178],"scenarios.":[180],"To":[181],"evaluate":[182],"designs,":[184],"employed":[186],"comprehensive":[188],"sequence-":[191],"metrics,":[194],"highlighting":[195],"benefits":[197],"methods":[200,207],"comparison":[202],"classical":[204],"identifying":[209],"deficiencies":[210],"improvement.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
