{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T06:12:34Z","timestamp":1775369554309,"version":"3.50.1"},"reference-count":79,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2017,10,23]],"date-time":"2017-10-23T00:00:00Z","timestamp":1508716800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004052","name":"KAUST","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61401131 and 61731008"],"award-info":[{"award-number":["61401131 and 61731008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive to experimentally determine the function of every enzyme. Therefore, computational enzyme function prediction has become increasingly important. In this paper, we develop such an approach, determining the enzyme function by predicting the Enzyme Commission number.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We propose an end-to-end feature selection and classification model training approach, as well as an automatic and robust feature dimensionality uniformization method, DEEPre, in the field of enzyme function prediction. Instead of extracting manually crafted features from enzyme sequences, our model takes the raw sequence encoding as inputs, extracting convolutional and sequential features from the raw encoding based on the classification result to directly improve the prediction performance. The thorough cross-fold validation experiments conducted on two large-scale datasets show that DEEPre improves the prediction performance over the previous state-of-the-art methods. In addition, our server outperforms five other servers in determining the main class of enzymes on a separate low-homology dataset. Two case studies demonstrate DEEPre\u2019s ability to capture the functional difference of enzyme isoforms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The server could be accessed freely at http:\/\/www.cbrc.kaust.edu.sa\/DEEPre.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx680","type":"journal-article","created":{"date-parts":[[2017,10,20]],"date-time":"2017-10-20T19:13:35Z","timestamp":1508526815000},"page":"760-769","source":"Crossref","is-referenced-by-count":245,"title":["DEEPre: sequence-based enzyme EC number prediction by deep learning"],"prefix":"10.1093","volume":"34","author":[{"given":"Yu","family":"Li","sequence":"first","affiliation":[{"name":"Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), Computer, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"}]},{"given":"Sheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), Computer, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"}]},{"given":"Ramzan","family":"Umarov","sequence":"additional","affiliation":[{"name":"Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), Computer, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"}]},{"given":"Bingqing","family":"Xie","sequence":"additional","affiliation":[{"name":"Computer Science Department, Illinois Institute of Technology, Chicago, IL, USA"}]},{"given":"Ming","family":"Fan","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China"}]},{"given":"Lihua","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China"}]},{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[{"name":"Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), Computer, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"}]}],"member":"286","published-online":{"date-parts":[[2017,10,23]]},"reference":[{"key":"2023012712400526600_btx680-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/3022670.2976746","article-title":"Tensorflow: Learning functions at scale","volume":"51","author":"Abadi","year":"2016","journal-title":"Acm Sigplan. 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