{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T16:13:18Z","timestamp":1770048798147,"version":"3.49.0"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,2,8]],"date-time":"2021-02-08T00:00:00Z","timestamp":1612742400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2016YFD0500406"],"award-info":[{"award-number":["2016YFD0500406"]}],"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":["32072900"],"award-info":[{"award-number":["32072900"]}],"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":["61702421"],"award-info":[{"award-number":["61702421"]}],"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":["U1811262"],"award-info":[{"award-number":["U1811262"]}],"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":["62076082"],"award-info":[{"award-number":["62076082"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Interactions between proteins and small molecule metabolites play vital roles in regulating protein functions and controlling various cellular processes. The activities of metabolic enzymes, transcription factors, transporters and membrane receptors can all be mediated through protein\u2013metabolite interactions (PMIs). Compared with the rich knowledge of protein\u2013protein interactions, little is known about PMIs. To the best of our knowledge, no existing database has been developed for collecting PMIs. The recent rapid development of large-scale mass spectrometry analysis of biomolecules has led to the discovery of large amounts of PMIs. Therefore, we developed the PMI-DB to provide a comprehensive and accurate resource of PMIs. A total of 49\u00a0785 entries were manually collected in the PMI-DB, corresponding to 23 small molecule metabolites, 9631 proteins and 4 species. Unlike other databases that only provide positive samples, the PMI-DB provides non-interaction between proteins and metabolites, which not only reduces the experimental cost for biological experimenters but also facilitates the construction of more accurate algorithms for researchers using machine learning. To show the convenience of the PMI-DB, we developed a deep learning-based method to predict PMIs in the PMI-DB and compared it with several methods. The experimental results show that the area under the curve and area under the precision-recall curve of our method are 0.88 and 0.95, respectively. Overall, the PMI-DB provides a user-friendly interface for browsing the biological functions of metabolites\/proteins of interest, and experimental techniques for identifying PMIs in different species, which provides important support for furthering the understanding of cellular processes. The PMI-DB is freely accessible at http:\/\/easybioai.com\/PMIDB.<\/jats:p>","DOI":"10.1093\/bib\/bbab014","type":"journal-article","created":{"date-parts":[[2021,1,12]],"date-time":"2021-01-12T01:41:33Z","timestamp":1610415693000},"source":"Crossref","is-referenced-by-count":67,"title":["Prediction and collection of protein\u2013metabolite interactions"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1913-081X","authenticated-orcid":false,"given":"Tianyi","family":"Zhao","sequence":"first","affiliation":[{"name":"The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Inner Mongolia, 010010, China"},{"name":"Department of Computer Science, Harbin Institute of Technology, Harbin, 150001, China"}]},{"given":"Jinxin","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Harbin Institute of Technology, Harbin, 150001, China"}]},{"given":"Xi","family":"Zeng","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, 710072, China"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, 710072, China"}]},{"given":"Sheng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430000, China"}]},{"given":"Tianyi","family":"Zang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Harbin Institute of Technology, Harbin, 150001, China"}]},{"given":"Jiajie","family":"Peng","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, 710072, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1731-5837","authenticated-orcid":false,"given":"Yang","family":"Yang","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Inner Mongolia, 010010, China"}]}],"member":"286","published-online":{"date-parts":[[2021,2,8]]},"reference":[{"key":"2021090815125058000_ref1","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/nrmicro3238","article-title":"Coordination of microbial metabolism","volume":"12","author":"Chubukov","year":"2014","journal-title":"Nat Rev Microbiol"},{"key":"2021090815125058000_ref2","doi-asserted-by":"crossref","first-page":"903","DOI":"10.15252\/msb.20167402","article-title":"Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli","volume":"13","author":"Kochanowski","year":"2017","journal-title":"Mol Syst 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