{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T13:19:29Z","timestamp":1783948769088,"version":"3.55.0"},"reference-count":58,"publisher":"American Chemical Society (ACS)","issue":"17","license":[{"start":{"date-parts":[[2025,8,25]],"date-time":"2025-08-25T00:00:00Z","timestamp":1756080000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,8,25]],"date-time":"2025-08-25T00:00:00Z","timestamp":1756080000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,8,25]],"date-time":"2025-08-25T00:00:00Z","timestamp":1756080000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"name":"Zhejiang Provincial Natural Science Foundation of China","award":["LHDMZ25H300001"],"award-info":[{"award-number":["LHDMZ25H300001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2025,9,8]]},"DOI":"10.1021\/acs.jcim.5c01713","type":"journal-article","created":{"date-parts":[[2025,8,25]],"date-time":"2025-08-25T19:38:14Z","timestamp":1756150694000},"page":"9061-9074","source":"Crossref","is-referenced-by-count":4,"title":["PepBAN: A Deep Learning Framework with Bilinear Attention and Adversarial Learning for Peptide\u2013Protein Interaction Prediction"],"prefix":"10.1021","volume":"65","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-4420-3295","authenticated-orcid":true,"given":"Shuaiyan","family":"Li","sequence":"first","affiliation":[{"name":"College of Pharmaceutical Sciences","place":["Hangzhou, China"]},{"name":"Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6893-2013","authenticated-orcid":true,"given":"Xiaorui","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences","place":["Hangzhou, China"]},{"name":"Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuchen","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences","place":["Hangzhou, China"]},{"name":"Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingxuan","family":"Ge","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences","place":["Hangzhou, China"]},{"name":"Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donghai","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences","place":["Hangzhou, China"]},{"name":"Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongxia","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences","place":["Hangzhou, China"]},{"name":"Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7227-2580","authenticated-orcid":true,"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences","place":["Hangzhou, China"]},{"name":"Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6242-4218","authenticated-orcid":true,"given":"Chang-Yu","family":"Hsieh","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences","place":["Hangzhou, China"]},{"name":"Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2025,8,25]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.3390\/molecules28135169"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-024-02036-3"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-020-00315-3"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1016\/j.molmet.2019.09.010"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1109\/JBHI.2024.3491318"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1186\/s12967-024-05372-8"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2020.2973091"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab340"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1007\/s11030-021-10217-3"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx335"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrp.2024.101980"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-022-03445-2"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","unstructured":"Zhai, S.; Zhao, H.; Wang, J.; Lin, S.; Liu, T.; Jiang, D.; Kang, Y.; Yao, X.; Hou, T. PepPCBench Is a Comprehensive Benchmark for Protein-Peptide Complex Structure Prediction 2025 10.1021\/acs.jcim.5c01084.","DOI":"10.1021\/acs.jcim.5c01084"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-025-02654-4"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07487-w"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c00976"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00836"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","unstructured":"Lin, Z.; Akin, H.; Rao, R.; Hie, B.; Zhu, Z.; Lu, W.; Costa, A.; dos, S.; Fazel-Zarandi, M.; Sercu, T.; Candido, S.; Rives, A. Language Models of Protein Sequences at the Scale of Evolution Enable Accurate Structure Prediction. 2022 10.1101\/2022.07.20.500902.","DOI":"10.1101\/2022.07.20.500902"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-56895-w"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.24314"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.12211\/2096-8280.2023-074"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz328"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0687-1"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2021.08.010"},{"key":"ref25\/cit25","unstructured":"Bepler, T.; Berger, B. Learning Protein Sequence Embeddings Using Information from Structure. 2019, arXiv:1902.08661. arXiv.org e-Printarchive. http:\/\/arxiv.org\/abs\/1902.08661.(accessed November 07, 2024)."},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25772-4"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3978"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1000"},{"key":"ref29\/cit29","unstructured":"Long, M.; Cao, Z.; Wang, J.; Jordan, M. I. Conditional Adversarial Domain Adaptation. 2018, arXiv:1705.10667. arXiv.org e-Printarchive. https:\/\/arxiv.org\/abs\/1705.10667."},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-022-00605-1"},{"key":"ref31\/cit31","unstructured":"Kim, J.H.; Jun, J.; Zhang, B.T. In  Bilinear Attention Networks, Proceedings of the 32nd International Conference on Neural Information Processing Systems; NIPS\u201918; Curran Associates Inc.: Red Hook, NY, USA, 2018; pp 1571\u20131581."},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-9504-2_2"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1039\/D1CB00154J"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-43214-1"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c01921"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl158"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0082138"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1016\/j.ins.2022.11.139"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1004"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-020-00456-1"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","unstructured":"Santry, D. J. In  Convolutional Neural Networks, Demystifying Deep Learning: An Introduction to the Mathematics of Neural Networks; IEEE, 2024; pp 111\u2013131 10.1002\/9781394205639.ch6.","DOI":"10.1002\/9781394205639.ch6"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","unstructured":"Ullanat, V.; Jing, B.; Sledzieski, S.; Berger, B. Learning the Language of Protein-Protein Interactions 2025, 10.1101\/2025.03.09.642188.","DOI":"10.1101\/2025.03.09.642188"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty535"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1109\/TNNLS.2025.3547300"},{"key":"ref45\/cit45","unstructured":"Ouyang, L.; Key, A. Maximum Mean Discrepancy for Generalization in the Presence of Distribution and Missingness Shift. 2021arXiv:2111.10344. arXiv.org e-Printarchive. https:\/\/arxiv.org\/abs\/2111.10344."},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpclett.3c02398"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1109\/TPAMI.2022.3225073"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx302"},{"key":"ref49\/cit49","unstructured":"Mikolov, T.; Chen, K.; Corrado, G.; Dean, J. Efficient Estimation of Word Representations in Vector Space. 2013 arXiv:1301.3781. arXiv.org e-Printarchive. https:\/\/arxiv.org\/abs\/1301.3781."},{"key":"ref50\/cit50","unstructured":"Ajakan, H.; Germain, P.; Larochelle, H.; Laviolette, F.; Marchand, M. Domain-Adversarial Neural Networks. 2015, arXiv:1412.4446. arXiv.org e-Printarchive. https:\/\/arxiv.org\/abs\/1412.4446."},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1106023109"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M809656200"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-7000-1_26"},{"key":"ref54\/cit54","unstructured":"Schr\u00f6dinger L. L. C.  AxPyMOL Molecular Graphics Plugin for Microsoft PowerPoint, Version\n1.8 2015."},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1923-7"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1016\/j.neucom.2023.127063"},{"key":"ref57\/cit57","unstructured":"Agarap, A. F. Deep Learning Using Rectified Linear Units (ReLU). 2019, arXiv:1803.08375. arXiv.org e-Printarchive. http:\/\/arxiv.org\/abs\/1803.08375(accessed June 27, 2024)."},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-031-54263-3_1"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c01713","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c01713","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,8]],"date-time":"2025-09-08T08:10:51Z","timestamp":1757319051000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.5c01713"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,25]]},"references-count":58,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2025,9,8]]}},"alternative-id":["10.1021\/acs.jcim.5c01713"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.5c01713","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,25]]}}}