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To overcome this limitation, in a novel end-to-end architecture (named FeatNN), we develop a coevolutionary strategy to jointly represent the structure and sequence features of proteins and ultimately optimize the mathematical models for predicting CPA. Furthermore, from the perspective of data-driven approach, we proposed a rational method that can utilize both high- and low-quality databases to optimize the accuracy and generalization ability of FeatNN in CPA prediction tasks. Notably, we visually interpret the feature interaction process between sequence and structure in the rationally designed architecture. As a result, FeatNN considerably outperforms the state-of-the-art (SOTA) baseline in virtual drug evaluation tasks, indicating the feasibility of this approach for practical use. FeatNN provides an outstanding method for higher CPA prediction accuracy and better generalization ability by efficiently representing multimodal information of proteins via a coevolutionary strategy.<\/jats:p>","DOI":"10.1093\/bib\/bbac628","type":"journal-article","created":{"date-parts":[[2022,12,26]],"date-time":"2022-12-26T11:20:39Z","timestamp":1672053639000},"source":"Crossref","is-referenced-by-count":7,"title":["Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionary strategy"],"prefix":"10.1093","volume":"24","author":[{"given":"Binjie","family":"Guo","sequence":"first","affiliation":[{"name":"Department of Neurobiology and Department of Rehabilitation Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang Province 310058 , China"},{"name":"Zhejiang University School of Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang Province 310058 , China"},{"name":"Liangzhu Laboratory , MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, , 1369 West Wenyi Road, Hangzhou 311121 , China"},{"name":"Zhejiang University , MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, , 1369 West Wenyi Road, Hangzhou 311121 , China"},{"name":"NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hanyu","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Neurobiology and Department of Rehabilitation Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang Province 310058 , China"},{"name":"Zhejiang University School of Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang Province 310058 , China"},{"name":"Liangzhu Laboratory , MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key 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Hangzhou 311121 , China"},{"name":"Zhejiang University , MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, , 1369 West Wenyi Road, Hangzhou 311121 , China"},{"name":"NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaodan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Neurobiology and Department of Rehabilitation Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang Province 310058 , China"},{"name":"Zhejiang University School of Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang Province 310058 , China"},{"name":"Liangzhu Laboratory , MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, , 1369 West Wenyi Road, Hangzhou 311121 , China"},{"name":"Zhejiang University , MOE 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Integration, State Key Laboratory of Brain-machine Intelligence, , 1369 West Wenyi Road, Hangzhou 311121 , China"},{"name":"NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanming","family":"Zuo","sequence":"additional","affiliation":[{"name":"Liangzhu Laboratory , MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, , 1369 West Wenyi Road, Hangzhou 311121 , China"},{"name":"Zhejiang University , MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, , 1369 West Wenyi Road, Hangzhou 311121 , China"},{"name":"NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yicheng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Neurobiology and Department of Rehabilitation Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang Province 310058 , China"},{"name":"Zhejiang University School of Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang Province 310058 , China"},{"name":"Liangzhu Laboratory , MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, , 1369 West Wenyi Road, Hangzhou 311121 , China"},{"name":"Zhejiang University , MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, , 1369 West Wenyi Road, Hangzhou 311121 , China"},{"name":"NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University , Hangzhou 310058 , 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