{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T04:12:23Z","timestamp":1790741543695,"version":"4.1.0"},"reference-count":56,"publisher":"Royal Society of Chemistry (RSC)","issue":"7","license":[{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22573016"],"award-info":[{"award-number":["22573016"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["rsc.org"],"crossmark-restriction":true},"short-container-title":["Chem. Sci."],"abstract":"<jats:p>A deep learning framework, DSSA-PPI, uses disentangled structure-sequence attention to accurately predict mutation-induced protein\u2013protein binding affinity changes, offering a powerful tool for protein engineering and drug discovery.<\/jats:p>","DOI":"10.1039\/d5sc08898d","type":"journal-article","created":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T23:41:19Z","timestamp":1766533279000},"page":"3719-3732","update-policy":"https:\/\/doi.org\/10.1039\/rsc_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["DSSA-PPI: enhancing binding affinity change prediction upon protein mutations using disentangled structure\u2013sequence aware attention"],"prefix":"10.1039","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-6442-4594","authenticated-orcid":false,"given":"Juhong","family":"Wu","sequence":"first","affiliation":[{"name":"College of Chemistry, Fuzhou University, Fuzhou 350116, Fujian, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiehui","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Chemistry, Fuzhou University, Fuzhou 350116, Fujian, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tian","family":"Liang","sequence":"additional","affiliation":[{"name":"College of Chemistry, Fuzhou University, Fuzhou 350116, Fujian, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongqi","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Chemistry, Fuzhou University, Fuzhou 350116, Fujian, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Chemistry, Fuzhou University, Fuzhou 350116, Fujian, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianyi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Jilin Medical University, Jilin 132013, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5079-350X","authenticated-orcid":false,"given":"Xianmin","family":"Feng","sequence":"additional","affiliation":[{"name":"Jilin Medical University, Jilin 132013, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Gao","sequence":"additional","affiliation":[{"name":"College of Chemistry, Fuzhou University, Fuzhou 350116, Fujian, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, Fujian, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8220-049X","authenticated-orcid":false,"given":"Jinyu","family":"Li","sequence":"additional","affiliation":[{"name":"College of Chemistry, Fuzhou University, Fuzhou 350116, Fujian, China"},{"name":"College of Biological and Pharmaceutical Engineering, Jilin Agricultural Science and Technology University, Jilin 132101, China"},{"name":"Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, Fujian, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"292","published-online":{"date-parts":[[2026]]},"reference":[{"key":"D5SC08898D\/cit1\/1","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/s41392-020-00315-3","volume":"5","author":"Lu","year":"2020","journal-title":"Signal Transduct. Targeted Ther."},{"key":"D5SC08898D\/cit2\/1","doi-asserted-by":"crossref","first-page":"115800","DOI":"10.1016\/j.biopha.2023.115800","volume":"168","author":"Qian","year":"2023","journal-title":"Biomed. Pharmacother."},{"key":"D5SC08898D\/cit3\/1","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/gene.2012.55","volume":"14","author":"Tuller","year":"2013","journal-title":"Gene Immun."},{"key":"D5SC08898D\/cit4\/1","doi-asserted-by":"crossref","first-page":"110136","DOI":"10.1016\/j.intimp.2023.110136","volume":"119","author":"Hong","year":"2023","journal-title":"Int. Immunopharmacol."},{"key":"D5SC08898D\/cit5\/1","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1016\/j.tem.2015.09.013","volume":"26","author":"Humphrey","year":"2015","journal-title":"Trends Endocrinol. Metab."},{"key":"D5SC08898D\/cit6\/1","doi-asserted-by":"crossref","first-page":"1434088","DOI":"10.3389\/fphar.2024.1434088","volume":"15","author":"Wu","year":"2024","journal-title":"Front. Pharmacol"},{"key":"D5SC08898D\/cit7\/1","doi-asserted-by":"crossref","first-page":"5416","DOI":"10.3390\/ijms22115416","volume":"22","author":"Petrosino","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"D5SC08898D\/cit8\/1","doi-asserted-by":"crossref","first-page":"1129709","DOI":"10.3389\/fphar.2023.1129709","volume":"14","author":"Song","year":"2023","journal-title":"Front. Pharmacol"},{"key":"D5SC08898D\/cit9\/1","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1038\/ng.3782","volume":"49","author":"Zhao","year":"2017","journal-title":"Nat. Genet."},{"key":"D5SC08898D\/cit10\/1","doi-asserted-by":"crossref","first-page":"110360","DOI":"10.1016\/j.intimp.2023.110360","volume":"120","author":"Qin","year":"2023","journal-title":"Int. Immunopharmacol."},{"key":"D5SC08898D\/cit11\/1","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1038\/nn.4589","volume":"20","author":"Geisheker","year":"2017","journal-title":"Nat. Neurosci."},{"key":"D5SC08898D\/cit12\/1","doi-asserted-by":"crossref","first-page":"109126","DOI":"10.1016\/j.intimp.2022.109126","volume":"111","author":"Hu","year":"2022","journal-title":"Int. Immunopharmacol."},{"key":"D5SC08898D\/cit13\/1","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1038\/nmeth.3027","volume":"11","author":"Fowler","year":"2014","journal-title":"Nat. Methods"},{"key":"D5SC08898D\/cit14\/1","doi-asserted-by":"crossref","first-page":"W382","DOI":"10.1093\/nar\/gki387","volume":"33","author":"Schymkowitz","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"D5SC08898D\/cit15\/1","doi-asserted-by":"crossref","first-page":"5389","DOI":"10.1021\/acs.jpcb.7b11367","volume":"122","author":"Barlow","year":"2018","journal-title":"J. Phys. Chem. B"},{"key":"D5SC08898D\/cit16\/1","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1007\/s11030-024-10908-7","volume":"29","author":"Xie","year":"2025","journal-title":"Mol. Divers."},{"key":"D5SC08898D\/cit17\/1","doi-asserted-by":"crossref","first-page":"9478","DOI":"10.1021\/acs.chemrev.9b00055","volume":"119","author":"Wang","year":"2019","journal-title":"Chem. Rev."},{"key":"D5SC08898D\/cit18\/1","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1093\/bioinformatics\/btaa761","volume":"37","author":"Li","year":"2021","journal-title":"Bioinformatics"},{"key":"D5SC08898D\/cit19\/1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13040-020-00231-w","volume":"13","author":"Abbasi","year":"2020","journal-title":"BioData Min."},{"key":"D5SC08898D\/cit20\/1","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/s42256-020-0149-6","volume":"2","author":"Wang","year":"2020","journal-title":"Nat. Mach. Intell."},{"key":"D5SC08898D\/cit21\/1","doi-asserted-by":"crossref","first-page":"6676","DOI":"10.1021\/acs.jcim.4c00976","volume":"64","author":"Wee","year":"2024","journal-title":"J. Chem. Inf. Model."},{"key":"D5SC08898D\/cit22\/1","doi-asserted-by":"crossref","first-page":"e1009284","DOI":"10.1371\/journal.pcbi.1009284","volume":"17","author":"Liu","year":"2021","journal-title":"PLoS Comput. Biol."},{"key":"D5SC08898D\/cit23\/1","doi-asserted-by":"crossref","first-page":"bbad310","DOI":"10.1093\/bib\/bbad310","volume":"24","author":"Yue","year":"2023","journal-title":"Brief. Bioinform."},{"key":"D5SC08898D\/cit24\/1","doi-asserted-by":"crossref","first-page":"2402918","DOI":"10.1002\/advs.202402918","volume":"11","author":"Li","year":"2024","journal-title":"Adv. Sci."},{"key":"D5SC08898D\/cit25\/1","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"D5SC08898D\/cit26\/1","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1126\/science.abj8754","volume":"373","author":"Baek","year":"2021","journal-title":"Science"},{"key":"D5SC08898D\/cit27\/1","first-page":"1","author":"Raouraoua","year":"2024","journal-title":"Nat. Comput. Sci."},{"key":"D5SC08898D\/cit28\/1","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1038\/s41597-023-02035-z","volume":"10","author":"Kilim","year":"2023","journal-title":"Sci. Data"},{"key":"D5SC08898D\/cit29\/1","volume-title":"Learning to Design Protein-Protein Interactions with Enhanced Generalization","author":"Bushuiev","year":"2024","unstructured":"A.Bushuiev ,  R.Bushuiev ,  P.Kouba ,  A.Filkin ,  M.Gabrielova ,  M.Gabriel ,  J.Sedlar ,  T.Pluskal ,  J.Damborsky ,  S.Mazurenko  and  J.Sivic ,  Learning to Design Protein-Protein Interactions with Enhanced Generalization ,  ICLR ,  2024 ,  https:\/\/openreview.net\/forum?id=xcMmebCT7s"},{"key":"D5SC08898D\/cit30\/1","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.1093\/bioinformatics\/btz829","volume":"36","author":"Jemimah","year":"2020","journal-title":"Bioinformatics"},{"key":"D5SC08898D\/cit31\/1","doi-asserted-by":"crossref","first-page":"btaf270","DOI":"10.1093\/bioinformatics\/btaf270","volume":"41","author":"Gurusinghe","year":"2025","journal-title":"Bioinformatics"},{"key":"D5SC08898D\/cit32\/1","volume-title":"Equiformer, Equivariant Graph Attention Transformer for 3D Atomistic Graphs","author":"Liao","year":"2023","unstructured":"Y.-L.Liao  and  T.Smidt ,  Equiformer, Equivariant Graph Attention Transformer for 3D Atomistic Graphs ,  ICLR ,  2023 ,  https:\/\/openreview.net\/forum?id=KwmPfARgOTD"},{"key":"D5SC08898D\/cit33\/1","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1002\/prot.22921","volume":"79","author":"Kellogg","year":"2011","journal-title":"Protein Struct. Funct. Bioinform."},{"key":"D5SC08898D\/cit34\/1","doi-asserted-by":"crossref","first-page":"6785","DOI":"10.1021\/ja809133u","volume":"131","author":"Manson","year":"2009","journal-title":"J. Am. Chem. Soc."},{"key":"D5SC08898D\/cit35\/1","doi-asserted-by":"crossref","first-page":"4578","DOI":"10.1021\/acs.jctc.1c00372","volume":"17","author":"Verkhivker","year":"2021","journal-title":"J. Chem. Theory Comput."},{"issue":"5","key":"D5SC08898D\/cit36\/1","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1006\/jmbi.1998.1978","volume":"281","author":"Bahar","year":"1998","journal-title":"J. Mol. Biol."},{"key":"D5SC08898D\/cit37\/1","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/S0006-3495(01)76033-X","volume":"80","author":"Atilgan","year":"2001","journal-title":"Biophys. J."},{"key":"D5SC08898D\/cit38\/1","doi-asserted-by":"crossref","first-page":"eadv9817","DOI":"10.1126\/science.adv9817","volume":"389","author":"Lewis","year":"2025","journal-title":"Science"},{"key":"D5SC08898D\/cit39\/1","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1038\/s41557-025-01874-0","volume":"17","author":"Charron","year":"2025","journal-title":"Nat. Chem."},{"key":"D5SC08898D\/cit40\/1","doi-asserted-by":"crossref","first-page":"3288","DOI":"10.1021\/acs.jctc.4c01620","volume":"21","author":"Jin","year":"2025","journal-title":"J. Chem. Theory Comput."},{"key":"D5SC08898D\/cit41\/1","doi-asserted-by":"crossref","first-page":"bbad491","DOI":"10.1093\/bib\/bbad491","volume":"25","author":"Tsishyn","year":"2024","journal-title":"Brief. Bioinform."},{"key":"D5SC08898D\/cit42\/1","volume-title":"ICML 2024 Workshop on Machine Learning for Life and Material Science","author":"Zhang","year":"2024","unstructured":"R.Zhang ,  N.Chen ,  F.Zhou  and  X.Gao ,  Navigating Trustworthiness of Deep Learning in \u0394\u0394G Prediction : Addressing Data Bias, Model Evaluation, and Interpretation , in  ICML 2024 Workshop on Machine Learning for Life and Material Science ,  2024 ,  https:\/\/openreview.net\/forum?id=XU1ACMwTlr"},{"key":"D5SC08898D\/cit43\/1","doi-asserted-by":"crossref","first-page":"23122","DOI":"10.1038\/s41598-024-72491-z","volume":"14","author":"Chi","year":"2024","journal-title":"Sci. Rep."},{"key":"D5SC08898D\/cit44\/1","doi-asserted-by":"crossref","first-page":"107918","DOI":"10.1016\/j.compbiomed.2024.107918","volume":"169","author":"Wee","year":"2024","journal-title":"Comput. Biol. Med."},{"key":"D5SC08898D\/cit45\/1","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1016\/j.cell.2020.08.012","volume":"182","author":"Starr","year":"2020","journal-title":"Cell"},{"key":"D5SC08898D\/cit46\/1","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.virol.2022.05.003","volume":"572","author":"Pond\u00e9","year":"2022","journal-title":"Virology"},{"key":"D5SC08898D\/cit47\/1","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/s41422-022-00644-8","volume":"32","author":"Lan","year":"2022","journal-title":"Cell Res."},{"key":"D5SC08898D\/cit48\/1","first-page":"e150","volume":"45","author":"Zhou","year":"2025","journal-title":"Arterioscler. Thromb. Vasc. Biol."},{"key":"D5SC08898D\/cit49\/1","doi-asserted-by":"crossref","first-page":"028","DOI":"10.1055\/a-1984-7021","volume":"43","author":"Koulas","year":"2023","journal-title":"H\u00e4mostaseologie"},{"key":"D5SC08898D\/cit50\/1","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1042\/BJ20071646","volume":"412","author":"Andersen","year":"2008","journal-title":"Biochem. J."},{"key":"D5SC08898D\/cit51\/1","doi-asserted-by":"crossref","first-page":"8868","DOI":"10.1021\/acs.jmedchem.5b01128","volume":"58","author":"Xu","year":"2015","journal-title":"J. Med. Chem."},{"key":"D5SC08898D\/cit52\/1","doi-asserted-by":"crossref","first-page":"e115872","DOI":"10.1371\/journal.pone.0115872","volume":"9","author":"Zhao","year":"2014","journal-title":"PLoS One"},{"key":"D5SC08898D\/cit53\/1","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1126\/science.add2187","volume":"378","author":"Dauparas","year":"2022","journal-title":"Science"},{"key":"D5SC08898D\/cit54\/1","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2410.21127","volume-title":"arXiv","author":"Tan","year":"2024","unstructured":"Y.Tan ,  R.Wang ,  B.Wu ,  L.Hong  and  B.Zhou ,  Retrieval-Enhanced Mutation Mastery: Augmenting Zero-Shot Prediction of Protein Language Model ,  arXiv ,  2024 , preprint, arXiv:2410.21127,  10.48550\/arXiv.2410.21127"},{"key":"D5SC08898D\/cit55\/1","doi-asserted-by":"crossref","first-page":"2404212","DOI":"10.1002\/advs.202404212","volume":"12","author":"Wang","year":"2025","journal-title":"Adv. Sci."},{"key":"D5SC08898D\/cit56\/1","doi-asserted-by":"publisher","DOI":"10.52202\/079017-1126","volume-title":"NeurIPS","author":"Li","year":"2024","unstructured":"M.Li ,  Y.Tan ,  X.Ma ,  B.Zhong ,  H.Yu ,  Z.Zhou ,  W.Ouyang ,  B.Zhou ,  P.Tan  and  L.Hong ,  ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention ,  NeurIPS ,  2024 ,  10.52202\/079017-1126"}],"container-title":["Chemical Science"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/pubs.rsc.org\/en\/content\/articlepdf\/2026\/SC\/D5SC08898D","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T21:21:12Z","timestamp":1782940872000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.rsc.org\/sc\/article\/17\/7\/3719-3732\/1248437"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":56,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2026,2,18]]}},"URL":"https:\/\/doi.org\/10.1039\/d5sc08898d","relation":{},"ISSN":["2041-6520","2041-6539"],"issn-type":[{"value":"2041-6520","type":"print"},{"value":"2041-6539","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026]]}}}