{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T16:02:52Z","timestamp":1770998572129,"version":"3.50.1"},"reference-count":101,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,12,12]],"date-time":"2023-12-12T00:00:00Z","timestamp":1702339200000},"content-version":"vor","delay-in-days":20,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61922073"],"award-info":[{"award-number":["61922073"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"2022 Tencent Rhino-Bird Research Elite Training Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Protein\u2013ligand binding affinity (PLBA) prediction is the fundamental task in drug discovery. Recently, various deep learning-based models predict binding affinity by incorporating the three-dimensional (3D) structure of protein\u2013ligand complexes as input and achieving astounding progress. However, due to the scarcity of high-quality training data, the generalization ability of current models is still limited. Although there is a vast amount of affinity data available in large-scale databases such as ChEMBL, issues such as inconsistent affinity measurement labels (i.e. IC50, Ki, Kd), different experimental conditions, and the lack of available 3D binding structures complicate the development of high-precision affinity prediction models using these data. To address these issues, we (i) propose Multi-task Bioassay Pre-training (MBP), a pre-training framework for structure-based PLBA prediction; (ii) construct a pre-training dataset called ChEMBL-Dock with more than 300k experimentally measured affinity labels and about 2.8M docked 3D structures. By introducing multi-task pre-training to treat the prediction of different affinity labels as different tasks and classifying relative rankings between samples from the same bioassay, MBP learns robust and transferrable structural knowledge from our new ChEMBL-Dock dataset with varied and noisy labels. Experiments substantiate the capability of MBP on the structure-based PLBA prediction task. To the best of our knowledge, MBP is the first affinity pre-training model and shows great potential for future development. MBP web-server is now available for free at: https:\/\/huggingface.co\/spaces\/jiaxianustc\/mbp.<\/jats:p>","DOI":"10.1093\/bib\/bbad451","type":"journal-article","created":{"date-parts":[[2023,12,12]],"date-time":"2023-12-12T17:46:52Z","timestamp":1702403212000},"source":"Crossref","is-referenced-by-count":15,"title":["Multi-task bioassay pre-training for protein-ligand binding affinity prediction"],"prefix":"10.1093","volume":"25","author":[{"given":"Jiaxian","family":"Yan","sequence":"first","affiliation":[{"name":"Anhui Province Key Lab of Big Data Analysis and Application, University of Science and Technology of China , JinZhai Road, 230026, Anhui , China"}]},{"given":"Zhaofeng","family":"Ye","sequence":"additional","affiliation":[{"name":"Tencent Quantum Laboratory , Tencent, Shennan Road, 518057, Guangdong , China"}]},{"given":"Ziyi","family":"Yang","sequence":"additional","affiliation":[{"name":"Tencent Quantum Laboratory , Tencent, Shennan Road, 518057, Guangdong , China"}]},{"given":"Chengqiang","family":"Lu","sequence":"additional","affiliation":[{"name":"Anhui Province Key Lab of Big Data Analysis and Application, University of Science and Technology of China , JinZhai Road, 230026, Anhui , China"}]},{"given":"Shengyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Tencent Quantum Laboratory , Tencent, Shennan Road, 518057, Guangdong , China"}]},{"given":"Qi","family":"Liu","sequence":"additional","affiliation":[{"name":"Anhui Province Key Lab of Big Data Analysis and Application, University of Science and Technology of China , JinZhai Road, 230026, Anhui , China"}]},{"given":"Jiezhong","family":"Qiu","sequence":"additional","affiliation":[{"name":"Tencent Quantum Laboratory , Tencent, Shennan Road, 518057, Guangdong , China"}]}],"member":"286","published-online":{"date-parts":[[2023,12,11]]},"reference":[{"key":"2024011119371894700_ref1","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/B978-0-12-819132-3.00014-2","volume-title":"Protein Homeostasis Diseases","author":"Rizzuti","year":"2020"},{"key":"2024011119371894700_ref2","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1186\/s12859-021-04466-0","article-title":"Binding affinity prediction for protein-ligand complex using deep attention mechanism based on intermolecular interactions","volume":"22","author":"Seo","year":"2021","journal-title":"BMC Bioinformatics"},{"key":"2024011119371894700_ref3","doi-asserted-by":"crossref","first-page":"2149","DOI":"10.1093\/bioinformatics\/btn409","article-title":"Protein-ligand interaction prediction: an improved chemogenomics 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