{"id":"https://openalex.org/W4400060352","doi":"https://doi.org/10.1021/acs.jcim.4c00678","title":"TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides","display_name":"TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides","publication_year":2024,"publication_date":"2024-06-26","ids":{"openalex":"https://openalex.org/W4400060352","doi":"https://doi.org/10.1021/acs.jcim.4c00678","pmid":"https://pubmed.ncbi.nlm.nih.gov/38920330"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c00678","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00678","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5114182789","display_name":"Nanqi Hong","orcid":null},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]},{"id":"https://openalex.org/I168879160","display_name":"Zhejiang University of Science and Technology","ror":"https://ror.org/05mx0wr29","country_code":"CN","type":"education","lineage":["https://openalex.org/I168879160"]},{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Nanqi Hong","raw_affiliation_strings":["College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang 310027, China","Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang 310027, China","institution_ids":["https://openalex.org/I168879160"]},{"raw_affiliation_string":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052900302","display_name":"Dejun Jiang","orcid":"https://orcid.org/0000-0002-2035-5074"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dejun Jiang","raw_affiliation_strings":["Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100407681","display_name":"Zhe Wang","orcid":"https://orcid.org/0000-0003-4102-1353"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]},{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe Wang","raw_affiliation_strings":["Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011434518","display_name":"Huiyong Sun","orcid":"https://orcid.org/0000-0002-7107-7481"},"institutions":[{"id":"https://openalex.org/I161716053","display_name":"China Pharmaceutical University","ror":"https://ror.org/01sfm2718","country_code":"CN","type":"education","lineage":["https://openalex.org/I161716053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huiyong Sun","raw_affiliation_strings":["Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu 210009, China"],"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu 210009, China","institution_ids":["https://openalex.org/I161716053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111317064","display_name":"Hao Luo","orcid":"https://orcid.org/0009-0001-0889-4905"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]},{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Luo","raw_affiliation_strings":["Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050719401","display_name":"Lingjie Bao","orcid":null},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]},{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lingjie Bao","raw_affiliation_strings":["Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026532752","display_name":"Mingli Song","orcid":"https://orcid.org/0000-0003-2621-6048"},"institutions":[{"id":"https://openalex.org/I168879160","display_name":"Zhejiang University of Science and Technology","ror":"https://ror.org/05mx0wr29","country_code":"CN","type":"education","lineage":["https://openalex.org/I168879160"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Mingli Song","raw_affiliation_strings":["College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang 310027, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang 310027, China","institution_ids":["https://openalex.org/I168879160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100624617","display_name":"Yu Kang","orcid":"https://orcid.org/0000-0002-0999-8802"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yu Kang","raw_affiliation_strings":["Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028525523","display_name":"Tingjun Hou","orcid":"https://orcid.org/0000-0001-7227-2580"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]},{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tingjun Hou","raw_affiliation_strings":["Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5026532752","https://openalex.org/A5028525523","https://openalex.org/A5100624617"],"corresponding_institution_ids":["https://openalex.org/I168879160","https://openalex.org/I4210123185","https://openalex.org/I76130692"],"apc_list":null,"apc_paid":null,"fwci":1.0002,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.74914144,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"64","issue":"13","first_page":"5016","last_page":"5027"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.996399998664856,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.995199978351593,"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/interpretability","display_name":"Interpretability","score":0.8312184810638428},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5798103213310242},{"id":"https://openalex.org/keywords/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.49428820610046387},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.460018128156662},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.4565962255001068},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4516517221927643},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43216049671173096},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35023167729377747},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3227415084838867},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.3079841136932373},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.1357254683971405}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8312184810638428},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5798103213310242},{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.49428820610046387},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.460018128156662},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.4565962255001068},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4516517221927643},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43216049671173096},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35023167729377747},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3227415084838867},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.3079841136932373},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.1357254683971405},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"D015789","descriptor_name":"HLA-A2 Antigen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015789","descriptor_name":"HLA-A2 Antigen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015789","descriptor_name":"HLA-A2 Antigen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015789","descriptor_name":"HLA-A2 Antigen","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015789","descriptor_name":"HLA-A2 Antigen","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015789","descriptor_name":"HLA-A2 Antigen","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c00678","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00678","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:38920330","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38920330","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4598670785","display_name":null,"funder_award_id":"92370130","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5087039848","display_name":null,"funder_award_id":"2022M722777","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G5662474503","display_name":null,"funder_award_id":"2230711","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7903508730","display_name":null,"funder_award_id":"22220102001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1965266522","https://openalex.org/W1969089800","https://openalex.org/W2005380527","https://openalex.org/W2012324563","https://openalex.org/W2019993505","https://openalex.org/W2028104451","https://openalex.org/W2063184115","https://openalex.org/W2073621589","https://openalex.org/W2081831455","https://openalex.org/W2082108597","https://openalex.org/W2083685984","https://openalex.org/W2090433023","https://openalex.org/W2094706980","https://openalex.org/W2097283546","https://openalex.org/W2106648157","https://openalex.org/W2112803219","https://openalex.org/W2143210482","https://openalex.org/W2148512505","https://openalex.org/W2159404298","https://openalex.org/W2164270482","https://openalex.org/W2234384516","https://openalex.org/W2271914738","https://openalex.org/W2295598076","https://openalex.org/W2305515617","https://openalex.org/W2334723342","https://openalex.org/W2589139221","https://openalex.org/W2743893844","https://openalex.org/W2762030706","https://openalex.org/W2898389621","https://openalex.org/W2949949116","https://openalex.org/W2951676304","https://openalex.org/W2953065444","https://openalex.org/W2971621113","https://openalex.org/W2974531988","https://openalex.org/W2995494055","https://openalex.org/W3004696891","https://openalex.org/W3021473997","https://openalex.org/W3024570138","https://openalex.org/W3030018498","https://openalex.org/W3087004338","https://openalex.org/W3098189759","https://openalex.org/W3122375914","https://openalex.org/W3156645689","https://openalex.org/W3171458272","https://openalex.org/W3203735717","https://openalex.org/W4200139236","https://openalex.org/W4220655797","https://openalex.org/W4231722547","https://openalex.org/W4241003864","https://openalex.org/W4245878933","https://openalex.org/W4247678459","https://openalex.org/W4284888788","https://openalex.org/W4385986396"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W4390569940","https://openalex.org/W4361193272","https://openalex.org/W2963326959","https://openalex.org/W4388685194","https://openalex.org/W2381567441","https://openalex.org/W3111171798"],"abstract_inverted_index":{"The":[0],"intricate":[1,218],"interaction":[2,187],"between":[3,99],"major":[4],"histocompatibility":[5],"complexes":[6],"(MHCs)":[7],"and":[8,23,89,101,120,153],"antigen":[9,41,102],"peptides":[10],"with":[11,115],"diverse":[12],"amino":[13,53],"acid":[14,54],"sequences":[15,114],"plays":[16],"a":[17,73,108],"pivotal":[18],"role":[19],"in":[20],"immune":[21],"responses":[22],"T":[24],"cell":[25],"activity.":[26],"In":[27,67],"recent":[28],"years,":[29],"deep":[30],"learning":[31],"(DL)-based":[32],"models":[33,48,143],"have":[34],"emerged":[35],"as":[36,150],"promising":[37],"tools":[38],"for":[39,60,223],"accelerating":[40],"peptide":[42],"screening.":[43],"However,":[44],"most":[45],"of":[46,132,174],"these":[47],"solely":[49],"rely":[50],"on":[51,107,134,145,158],"one-dimensional":[52],"sequences,":[55],"overlooking":[56],"crucial":[57],"information":[58,92],"required":[59],"the":[61,97,129,135,159,175,179,186,195,204],"three-dimensional":[62],"(3-D)":[63],"space":[64],"binding":[65,117,215],"process.":[66],"this":[68],"study,":[69],"we":[70],"propose":[71],"TransfIGN,":[72],"structure-based":[74],"DL":[75],"model":[76],"that":[77],"is":[78],"inspired":[79],"by":[80,191],"our":[81,165,192],"previously":[82],"developed":[83],"framework,":[84],"Interaction":[85],"Graph":[86],"Network":[87],"(IGN),":[88],"incorporates":[90],"sequence":[91],"from":[93],"transformers":[94],"to":[95,207,213],"predict":[96],"interactions":[98,197],"HLA-A*02:01":[100],"peptides.":[103],"Our":[104],"model,":[105],"trained":[106,144],"comprehensive":[109],"data":[110,137,147,163],"set":[111],"containing":[112],"61,816":[113],"9051":[116],"affinity":[118],"labels":[119],"56,848":[121],"eluted":[122],"ligand":[123],"labels,":[124],"achieves":[125],"an":[126],"area":[127],"under":[128],"curve":[130],"(AUC)":[131],"0.893":[133],"binary":[136],"set,":[138],"better":[139,171],"than":[140,172],"state-of-the-art":[141],"sequence-based":[142],"larger":[146],"sets":[148],"such":[149],"NetMHCpan4.1,":[151],"ANN,":[152],"TransPHLA.":[154],"Furthermore,":[155],"when":[156],"evaluated":[157],"IEDB":[160,180],"weekly":[161],"benchmark":[162],"sets,":[164],"predictions":[166],"(AUC":[167,182],"=":[168,183],"0.816)":[169],"are":[170],"those":[173],"recommended":[176],"methods":[177],"like":[178],"consensus":[181],"0.795).":[184],"Notably,":[185],"weight":[188],"matrices":[189],"generated":[190],"method":[193],"highlight":[194],"strong":[196],"at":[198],"specific":[199],"positions":[200],"within":[201],"peptides,":[202],"emphasizing":[203],"model's":[205],"ability":[206],"provide":[208],"physical":[209],"interpretability.":[210],"This":[211],"capability":[212],"unveil":[214],"mechanisms":[216],"through":[217],"structural":[219],"features":[220],"holds":[221],"promise":[222],"new":[224],"immunotherapeutic":[225],"avenues.":[226]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2025-12-26T23:08:49.675405","created_date":"2025-10-10T00:00:00"}
