{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,4]],"date-time":"2025-10-04T18:26:35Z","timestamp":1759602395282,"version":"3.41.2"},"reference-count":32,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,10,1]],"date-time":"2020-10-01T00:00:00Z","timestamp":1601510400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"International Partnership Programme of Chinese Academy of Sciences of China","award":["153D31KYSB20170121"],"award-info":[{"award-number":["153D31KYSB20170121"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31700081, 31570092"],"award-info":[{"award-number":["31700081, 31570092"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the Natural Science Foundation of Tianjin","award":["15JCYBJC54300"],"award-info":[{"award-number":["15JCYBJC54300"]}]},{"name":"Scientific Research Conditions and Technical Support System Programme","award":["KFJ-BRP-009"],"award-info":[{"award-number":["KFJ-BRP-009"]}]},{"name":"National Key Research and Development Programme of China","award":["2019YFA0904300,2018YFA0900700,2017YFC1601702"],"award-info":[{"award-number":["2019YFA0904300,2018YFA0900700,2017YFC1601702"]}]},{"name":"CAS STS programme","award":["QYZDB-SSW-SMC012"],"award-info":[{"award-number":["QYZDB-SSW-SMC012"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Addition of chemical structural information in enzymatic reactions has proven to be significant for accurate enzyme function prediction. However, such chemical data lack systematic feature mining and hardly exist in enzyme-related databases. Therefore, global mining of enzymatic reactions will offer a unique landscape for researchers to understand the basic functional mechanisms of natural bioprocesses and facilitate enzyme function annotation. Here, we established a new knowledge base called EnzyMine, through which we propose to elucidate enzymatic reaction features and then link them with sequence and structural annotations. EnzyMine represents an advanced database that extends enzyme knowledge by incorporating reaction chemical feature strategies, strengthening the connectivity between enzyme and metabolic reactions. Therefore, it has the potential to reveal many new metabolic pathways involved with given enzymes, as well as expand enzyme function annotation.<\/jats:p>\n               <jats:p>Database URL: http:\/\/www.rxnfinder.org\/enzymine\/<\/jats:p>","DOI":"10.1093\/database\/baaa065","type":"journal-article","created":{"date-parts":[[2020,8,4]],"date-time":"2020-08-04T19:16:59Z","timestamp":1596568619000},"source":"Crossref","is-referenced-by-count":11,"title":["EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature"],"prefix":"10.1093","volume":"2023","author":[{"given":"Dandan","family":"Sun","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200333, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xingxiang","family":"Cheng","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200333, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Tian","sequence":"additional","affiliation":[{"name":"School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University , Wuhan, Hubei 430023, China and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaozhen","family":"Ding","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200333, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dachuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200333, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengli","family":"Cai","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200333, P. R. China"},{"name":"Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qian-nan","family":"Hu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200333, P. R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,10,1]]},"reference":[{"key":"2023122906461074700_R1","doi-asserted-by":"crossref","first-page":"7542","DOI":"10.1093\/nar\/gky537","article-title":"Fast automated reconstruction of genome-scale metabolic models for microbial species and communities","volume":"46","author":"Machado","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023122906461074700_R2","doi-asserted-by":"crossref","first-page":"W291","DOI":"10.1093\/nar\/gkx366","article-title":"COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information","volume":"45","author":"Zhang","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2023122906461074700_R3","doi-asserted-by":"crossref","first-page":"2687","DOI":"10.1093\/bioinformatics\/bts510","article-title":"EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes","volume":"28","author":"Kumar","year":"2012","journal-title":"Bioinformatics"},{"key":"2023122906461074700_R4","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1093\/bioinformatics\/btx680","article-title":"DEEPre: sequence-based enzyme EC number prediction by deep learning","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2023122906461074700_R5","doi-asserted-by":"crossref","first-page":"D289","DOI":"10.1093\/nar\/gkw1098","article-title":"CATH: an expanded resource to predict protein function through structure and sequence","volume":"45","author":"Dawson","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2023122906461074700_R6","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gks1067","article-title":"New and continuing developments at PROSITE","volume":"41","author":"Sigrist","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023122906461074700_R7","doi-asserted-by":"crossref","first-page":"D618","DOI":"10.1093\/nar\/gkx1012","article-title":"Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites","volume":"46","author":"Ribeiro","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023122906461074700_R8","doi-asserted-by":"crossref","first-page":"D310","DOI":"10.1093\/nar\/gkt1242","article-title":"SCOP2 prototype: a new approach to protein structure mining","volume":"42","author":"Andreeva","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023122906461074700_R9","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: a hub for protein information","volume":"43","author":"Bateman","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2023122906461074700_R10","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023122906461074700_R11","doi-asserted-by":"crossref","first-page":"1833","DOI":"10.1021\/acs.jcim.9b00877","article-title":"Exploration and evaluation of machine learning-based models for predicting enzymatic reactions","volume":"60","author":"Watanabe","year":"2020","journal-title":"J. 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