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Most methods follow the canonical paradigm that processes the inputs of the protein (target) and the ligand (drug) separately and then combines them together. In this study we demonstrate, surprisingly, that a model is able to achieve even superior performance without access to any protein-sequence-related information. Instead, a protein is characterized completely by the ligands that it interacts. Specifically, we treat different proteins separately, which are jointly trained in a multi-head manner, so as to learn a robust and universal representation of ligands that is generalizable across proteins. Empirical evidences show that the novel paradigm outperforms its competitive sequence-based counterpart, with the Mean Squared Error (MSE) of 0.4261 versus 0.7612 and the R-Square of 0.7984 versus 0.6570 compared with DeepAffinity. We also investigate the transfer learning scenario where unseen proteins are encountered after the initial training, and the cross-dataset evaluation for prospective studies. The results reveals the robustness of the proposed model in generalizing to unseen proteins as well as in predicting future data. Source codes and data are available at https:\/\/github.com\/huzqatpku\/SAM-DTA.<\/jats:p>","DOI":"10.1093\/bib\/bbac533","type":"journal-article","created":{"date-parts":[[2022,12,22]],"date-time":"2022-12-22T08:52:17Z","timestamp":1671699137000},"source":"Crossref","is-referenced-by-count":12,"title":["SAM-DTA: a sequence-agnostic model for drug\u2013target binding affinity prediction"],"prefix":"10.1093","volume":"24","author":[{"given":"Zhiqiang","family":"Hu","sequence":"first","affiliation":[{"name":"SenseTime Research , Shanghai, 201103, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenfeng","family":"Liu","sequence":"additional","affiliation":[{"name":"Shanghai Matwings Technology Co. , Ltd., Shanghai, 200240, China"},{"name":"Department of Computer Science and Engineering , East China University of Science and Technology, Shanghai 200237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenbin","family":"Zhang","sequence":"additional","affiliation":[{"name":"SenseTime Research , Shanghai, 201103, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiawen","family":"Huang","sequence":"additional","affiliation":[{"name":"Shanghai Matwings Technology Co. , Ltd., Shanghai, 200240, China"},{"name":"Department of Computer Science and Engineering , East China University of Science and Technology, Shanghai 200237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaoting","family":"Zhang","sequence":"additional","affiliation":[{"name":"SenseTime Research , Shanghai, 201103, China"},{"name":"Shanghai Artificial Intelligence Laboratory , Shanghai 200232, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huiqun","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering , East China University of Science and Technology, Shanghai 200237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Xiong","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Biotechnology , Shanghai Jiao Tong University, Shanghai 200240, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Liu","sequence":"additional","affiliation":[{"name":"Shanghai Matwings Technology Co. , Ltd., Shanghai, 200240, China"},{"name":"Institute of Natural Sciences , Shanghai Jiao Tong University, Shanghai 200240, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Song","family":"Ke","sequence":"additional","affiliation":[{"name":"Shanghai Matwings Technology Co. , Ltd., Shanghai, 200240, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liang","family":"Hong","sequence":"additional","affiliation":[{"name":"School of Pharmacy , Shanghai Jiao Tong University, Shanghai 200240, China"},{"name":"School of Physics and Astronomy , Shanghai Jiao Tong University, Shanghai 200240, China"},{"name":"Institute of Natural Sciences , Shanghai Jiao Tong University, Shanghai 200240, China"},{"name":"Shanghai Artificial Intelligence Laboratory , Shanghai 200232, China"},{"name":"School of Life Sciences and Biotechnology , Shanghai Jiao Tong University, Shanghai 200240, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,12,21]]},"reference":[{"issue":"1","key":"2023011917143824600_ref1","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.healthpol.2010.12.002","article-title":"The cost of drug development: a systematic review","volume":"100","author":"Morgan","year":"2011","journal-title":"Health Policy"},{"issue":"11","key":"2023011917143824600_ref2","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1007\/s40273-021-01065-y","article-title":"How much does it cost to research and develop a new drug? 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