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However, the reliable acquisition of experimental GPCRs structures is hindered by their lipid-embedded conformations. Traditional protein\u2013ligand interaction models falter in GPCR\u2013drug interactions, caused by limited and low-quality structures. Generalized models, trained on soluble protein\u2013ligand pairs, are also inadequate. To address these issues, we developed two models, DeepGPCR_BC for binary classification and DeepGPCR_RG for affinity prediction. These models use non-structural GPCR\u2013ligand interaction data, leveraging graph convolutional networks and mol2vec techniques to represent binding pockets and ligands as graphs. This approach significantly speeds up predictions while preserving critical physical\u2013chemical and spatial information. In independent tests, DeepGPCR_BC surpassed Autodock Vina and Schr\u00f6dinger Dock with an area under the curve of 0.72, accuracy of 0.68 and true positive rate of 0.73, whereas DeepGPCR_RG demonstrated a Pearson correlation of 0.39 and root mean squared error of 1.34. We applied these models to screen drug candidates for GPR35 (Q9HC97), yielding promising results with three (F545-1970, K297-0698, S948-0241) out of eight candidates. Furthermore, we also successfully obtained six active inhibitors for GLP-1R. Our GPCR-specific models pave the way for efficient and accurate large-scale virtual screening, potentially revolutionizing drug discovery in the GPCR field.<\/jats:p>","DOI":"10.1093\/bib\/bbae281","type":"journal-article","created":{"date-parts":[[2024,5,29]],"date-time":"2024-05-29T18:03:24Z","timestamp":1717005804000},"source":"Crossref","is-referenced-by-count":22,"title":["Revolutionizing GPCR\u2013ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2133-1768","authenticated-orcid":false,"given":"Haiping","family":"Zhang","sequence":"first","affiliation":[{"name":"Faculty of Synthetic Biology and Institute of Synthetic Biology , Shenzhen Institute of Advanced Technology, , No. 1068 Xueyuan Boulevard, Nanshan District, Shenzhen 518055, Guangdong Province , China"},{"name":"Chinese Academy of Sciences , Shenzhen Institute of Advanced Technology, , No. 1068 Xueyuan Boulevard, Nanshan District, Shenzhen 518055, Guangdong Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongjie","family":"Fan","sequence":"additional","affiliation":[{"name":"Ganjiang Chinese Medicine Innovation Center , Xinqizhou East Road 888, Ganjiang New Area, Nanchang 330000 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jixia","family":"Wang","sequence":"additional","affiliation":[{"name":"Ganjiang Chinese Medicine Innovation Center , Xinqizhou East Road 888, Ganjiang New Area, Nanchang 330000 , China"},{"name":"CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, , No. 457 Zhongshan Road, Dalian 116023 , China"},{"name":"Chinese Academy of Sciences , Dalian Institute of Chemical Physics, , No. 457 Zhongshan Road, Dalian 116023 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tao","family":"Hou","sequence":"additional","affiliation":[{"name":"Ganjiang Chinese Medicine Innovation Center , Xinqizhou East Road 888, Ganjiang New Area, Nanchang 330000 , China"},{"name":"CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, , No. 457 Zhongshan Road, Dalian 116023 , China"},{"name":"Chinese Academy of Sciences , Dalian Institute of Chemical Physics, , No. 457 Zhongshan Road, Dalian 116023 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Konda Mani","family":"Saravanan","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Bharath Institute of Higher Education and Research , Agharam Road 173, Selaiyur, Chennai, Tamil Nadu 600073 , India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Xia","sequence":"additional","affiliation":[{"name":"Faculty of Synthetic Biology and Institute of Synthetic Biology , Shenzhen Institute of Advanced Technology, , No. 1068 Xueyuan Boulevard, Nanshan District, Shenzhen 518055, Guangdong Province , China"},{"name":"Chinese Academy of Sciences , Shenzhen Institute of Advanced Technology, , No. 1068 Xueyuan Boulevard, Nanshan District, Shenzhen 518055, Guangdong Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hei Wun","family":"Kan","sequence":"additional","affiliation":[{"name":"Faculty of Synthetic Biology and Institute of Synthetic Biology , Shenzhen Institute of Advanced Technology, , No. 1068 Xueyuan Boulevard, Nanshan District, Shenzhen 518055, Guangdong Province , China"},{"name":"Chinese Academy of Sciences , Shenzhen Institute of Advanced Technology, , No. 1068 Xueyuan Boulevard, Nanshan District, Shenzhen 518055, Guangdong Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junxin","family":"Li","sequence":"additional","affiliation":[{"name":"Shenzhen Laboratory of Human Antibody Engineering , Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, , No. 1068 Xueyuan Boulevard, Nanshan District, Shenzhen 518055, Guangdong Province , China"},{"name":"Chinese Academy of Sciences , Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, , No. 1068 Xueyuan Boulevard, Nanshan District, Shenzhen 518055, Guangdong Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John Z H","family":"Zhang","sequence":"additional","affiliation":[{"name":"Faculty of Synthetic Biology and Institute of Synthetic Biology , Shenzhen Institute of Advanced Technology, , No. 1068 Xueyuan Boulevard, Nanshan District, Shenzhen 518055, Guangdong Province , China"},{"name":"Chinese Academy of Sciences , Shenzhen Institute of Advanced Technology, , No. 1068 Xueyuan Boulevard, Nanshan District, Shenzhen 518055, Guangdong Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinmiao","family":"Liang","sequence":"additional","affiliation":[{"name":"Ganjiang Chinese Medicine Innovation Center , Xinqizhou East Road 888, Ganjiang New Area, Nanchang 330000 , China"},{"name":"CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics, , No. 457 Zhongshan Road, Dalian 116023 , China"},{"name":"Chinese Academy of Sciences , Dalian Institute of Chemical Physics, , No. 457 Zhongshan Road, Dalian 116023 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Chen","sequence":"additional","affiliation":[{"name":"Ganjiang Chinese Medicine Innovation Center , Xinqizhou East Road 888, Ganjiang New Area, Nanchang 330000 , China"},{"name":"CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian 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