{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T21:01:05Z","timestamp":1775509265176,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T00:00:00Z","timestamp":1724112000000},"content-version":"vor","delay-in-days":26,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2022YFA0913000"],"award-info":[{"award-number":["2022YFA0913000"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22208211"],"award-info":[{"award-number":["22208211"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22378263"],"award-info":[{"award-number":["22378263"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Turnover numbers (kcat), which indicate an enzyme's catalytic efficiency, have a wide range of applications in fields including protein engineering and synthetic biology. Experimentally measuring the enzymes' kcat is always time-consuming. Recently, the prediction of kcat using deep learning models has mitigated this problem. However, the accuracy and robustness in kcat prediction still needs to be improved significantly, particularly when dealing with enzymes with low sequence similarity compared to those within the training dataset. Herein, we present DeepEnzyme, a cutting-edge deep learning model that combines the most recent Transformer and Graph Convolutional Network (GCN) to capture the information of both the sequence and 3D-structure of a protein. To improve the prediction accuracy, DeepEnzyme was trained by leveraging the integrated features from both sequences and 3D-structures. Consequently, DeepEnzyme exhibits remarkable robustness when processing enzymes with low sequence similarity compared to those in the training dataset by utilizing additional features from high-quality protein 3D-structures. DeepEnzyme also makes it possible to evaluate how point mutations affect the catalytic activity of the enzyme, which helps identify residue sites that are crucial for the catalytic function. In summary, DeepEnzyme represents a pioneering effort in predicting enzymes' kcat values with improved accuracy and robustness compared to previous algorithms. This advancement will significantly contribute to our comprehension of enzyme function and its evolutionary patterns across species.<\/jats:p>","DOI":"10.1093\/bib\/bbae409","type":"journal-article","created":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T09:39:53Z","timestamp":1722764393000},"source":"Crossref","is-referenced-by-count":36,"title":["DeepEnzyme: a robust deep learning model for improved enzyme turnover number prediction by utilizing features of protein 3D-structures"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8789-7126","authenticated-orcid":false,"given":"Tong","family":"Wang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Microbial Metabolism , School of Life Science and Biotechnology, , 800 Dongchuan RD. Minhang District, Shanghai 200240 ,","place":["China"]},{"name":"Shanghai Jiao Tong University , School of Life Science and Biotechnology, , 800 Dongchuan RD. Minhang District, Shanghai 200240 ,","place":["China"]},{"name":"College of Science, Chongqing University of Technology , 69 Hongguang Avenue, Banan District, Chongqing 400054 ,","place":["China"]}]},{"given":"Guangming","family":"Xiang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Metabolism , School of Life Science and Biotechnology, , 800 Dongchuan RD. Minhang District, Shanghai 200240 ,","place":["China"]},{"name":"Shanghai Jiao Tong University , School of Life Science and Biotechnology, , 800 Dongchuan RD. Minhang District, Shanghai 200240 ,","place":["China"]}]},{"given":"Siwei","family":"He","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Metabolism , School of Life Science and Biotechnology, , 800 Dongchuan RD. Minhang District, Shanghai 200240 ,","place":["China"]},{"name":"Shanghai Jiao Tong University , School of Life Science and Biotechnology, , 800 Dongchuan RD. Minhang District, Shanghai 200240 ,","place":["China"]}]},{"given":"Liyun","family":"Su","sequence":"additional","affiliation":[{"name":"College of Science, Chongqing University of Technology , 69 Hongguang Avenue, Banan District, Chongqing 400054 ,","place":["China"]}]},{"given":"Yuguang","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Natural Sciences , School of Mathematical Sciences, Zhangjiang Institute of Advanced Study, , 800 Dongchuan RD. Minhang District, Shanghai 200240 ,","place":["China"]},{"name":"Shanghai Jiao Tong University , School of Mathematical Sciences, Zhangjiang Institute of Advanced Study, , 800 Dongchuan RD. Minhang District, Shanghai 200240 ,","place":["China"]},{"name":"Shanghai Artificial Intelligence Laboratory , 701 Yunjin Road, Xuhui District, Shanghai 200237 ,","place":["China"]}]},{"given":"Xuefeng","family":"Yan","sequence":"additional","affiliation":[{"name":"Key Laboratory of Smart Manufacturing in Energy Chemical Process , Ministry of Education, , 130 Meilong Road, Xuhui District, Shanghai 200237 ,","place":["China"]},{"name":"East China University of Science and Technology , Ministry of Education, , 130 Meilong Road, Xuhui District, Shanghai 200237 ,","place":["China"]},{"name":"State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , 130 Meilong Road, Xuhui District, Shanghai 200237 ,","place":["China"]}]},{"given":"Hongzhong","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Metabolism , School of Life Science and Biotechnology, , 800 Dongchuan RD. 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