{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T19:46:56Z","timestamp":1784317616084,"version":"3.55.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,4,29]],"date-time":"2023-04-29T00:00:00Z","timestamp":1682726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81671807"],"award-info":[{"award-number":["81671807"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82072078"],"award-info":[{"award-number":["82072078"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Research and Developement Program of Jiangsu Province","award":["BE2020777"],"award-info":[{"award-number":["BE2020777"]}]},{"name":"Key Research and Developement Program of Jiangsu Province","award":["SBE2020741118"],"award-info":[{"award-number":["SBE2020741118"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2242018K3DN05"],"award-info":[{"award-number":["2242018K3DN05"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Scientific Research Project of Jiangsu Health Commission","award":["ZDA2020012"],"award-info":[{"award-number":["ZDA2020012"]}]},{"name":"Shared Service Platform of Data Computing Center, Southeast University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Peptide-major histocompatibility complex I (MHC I) binding affinity prediction is crucial for vaccine development, but existing methods face limitations such as small datasets, model overfitting due to excessive parameters and suboptimal performance. Here, we present STMHCPan (STAR-MHCPan), an open-source package based on the Star-Transformer model, for MHC I binding peptide prediction. Our approach introduces an attention mechanism to improve the deep learning network architecture and performance in antigen prediction. Compared with classical deep learning algorithms, STMHCPan exhibits improved performance with fewer parameters in receptor affinity training. Furthermore, STMHCPan outperforms existing ligand benchmark datasets identified by mass spectrometry. It can also handle peptides of arbitrary length and is highly scalable for predicting T-cell responses. Our software is freely available for use, training and extension through Github (https:\/\/github.com\/Luckysoutheast\/STMHCPan.git).<\/jats:p>","DOI":"10.1093\/bib\/bbad164","type":"journal-article","created":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T03:29:41Z","timestamp":1682911781000},"source":"Crossref","is-referenced-by-count":25,"title":["STMHCpan, an accurate Star-Transformer-based extensible framework for predicting MHC I allele binding peptides"],"prefix":"10.1093","volume":"24","author":[{"given":"Zheng","family":"Ye","sequence":"first","affiliation":[{"name":"State Key Laboratory of Bioelectronics , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"},{"name":"Southeast University , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaohao","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioelectronics , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"},{"name":"Southeast University , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xue","family":"Mi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioelectronics , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"},{"name":"Southeast University , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baoyi","family":"Shao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioelectronics , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"},{"name":"Southeast University , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhu","family":"Dai","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioelectronics , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"},{"name":"Southeast University , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecoloty, Zhongda Hospital, School of Medicine, Southeast University , Nanjing 210009 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Songwei","family":"Feng","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecoloty, Zhongda Hospital, School of Medicine, Southeast University , Nanjing 210009 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Sun","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioelectronics , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"},{"name":"Southeast University , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecoloty, Zhongda Hospital, School of Medicine, Southeast University , Nanjing 210009 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongdang","family":"Xiao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioelectronics , School of Biological Science and Medical Engineering, , Nanjing, Jiangsu 210096 , China"},{"name":"Southeast University , School of Biological Science and Medical 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