{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T14:48:54Z","timestamp":1776696534198,"version":"3.51.2"},"reference-count":40,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,3,26]],"date-time":"2024-03-26T00:00:00Z","timestamp":1711411200000},"content-version":"vor","delay-in-days":85,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"HZAU-AGIS Cooperation Fund","award":["SZYJY2022027"],"award-info":[{"award-number":["SZYJY2022027"]}]},{"DOI":"10.13039\/501100003819","name":"Natural Science Foundation of Hubei Province","doi-asserted-by":"publisher","award":["2022CFB659"],"award-info":[{"award-number":["2022CFB659"]}],"id":[{"id":"10.13039\/501100003819","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32072323, 32073022, 31772083"],"award-info":[{"award-number":["32072323, 32073022, 31772083"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"HZAU-AGIS Cooperation Fund","award":["SZYJY2022027"],"award-info":[{"award-number":["SZYJY2022027"]}]},{"DOI":"10.13039\/501100003819","name":"Natural Science Foundation of Hubei Province","doi-asserted-by":"publisher","award":["2022CFB659"],"award-info":[{"award-number":["2022CFB659"]}],"id":[{"id":"10.13039\/501100003819","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32072323, 32073022, 31772083"],"award-info":[{"award-number":["32072323, 32073022, 31772083"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>\u2018Superbugs\u2019 have received increasing attention from researchers, such as ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.), which directly led to about 1\u00a0270\u00a0000 death cases in 2019. Recently, phage peptidoglycan hydrolases (PGHs)\u2013derived antimicrobial peptides were proposed as new antibacterial agents against multidrug-resistant bacteria. However, there is still a lack of methods for mining antimicrobial peptides based on phages or phage PGHs. Here, by using a collection of 6809 genomes of ESKAPE isolates and corresponding phages in public databases, based on a unified annotation process of all the genomes, PGHs were systematically identified, from which peptides were mined. As a result, a total of 12\u00a0067\u00a0248 peptides with high antibacterial activities were respectively determined. A user-friendly tool was developed to predict the phage PGHs\u2013derived antimicrobial peptides from customized genomes, which also allows the calculation of peptide phylogeny, physicochemical properties, and secondary structure. Finally, a user-friendly and intuitive database, ESKtides ( http:\/\/www.phageonehealth.cn:9000\/ESKtides), was designed for data browsing, searching and downloading, which provides a rich peptide library based on ESKAPE prophages and phages.<\/jats:p>\n               <jats:p>Database URL: \u00a010.1093\/database\/baae022<\/jats:p>","DOI":"10.1093\/database\/baae022","type":"journal-article","created":{"date-parts":[[2024,3,26]],"date-time":"2024-03-26T21:14:51Z","timestamp":1711487691000},"source":"Crossref","is-referenced-by-count":12,"title":["ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides"],"prefix":"10.1093","volume":"2024","author":[{"given":"Hongfang","family":"Wu","sequence":"first","affiliation":[{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University National Key Laboratory of Agricultural Microbiology, , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"College of Food Science and Technology, Huazhong Agricultural University Hubei Hongshan Laboratory, , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rongxian","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University National Key Laboratory of Agricultural Microbiology, , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"College of Food Science and Technology, Huazhong Agricultural University Hubei Hongshan Laboratory, , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuejian","family":"Li","sequence":"additional","affiliation":[{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University National Key Laboratory of Agricultural Microbiology, , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"College of Food Science and Technology, Huazhong Agricultural University Hubei Hongshan Laboratory, , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"College of Informatics, Huazhong Agricultural University , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University National Key Laboratory of Agricultural Microbiology, , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"College of Food Science and Technology, Huazhong Agricultural University Hubei Hongshan Laboratory, , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8030-5346","authenticated-orcid":false,"given":"Jianwei","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanbo","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Informatics, Huazhong Agricultural University , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Wan","sequence":"additional","affiliation":[{"name":"College of Food Science and Technology, Huazhong Agricultural University Hubei Hongshan Laboratory, , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Fisheries, Huazhong Agricultural University , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huanchun","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University National Key Laboratory of Agricultural Microbiology, , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"College of Veterinary Medicine, Huazhong Agricultural University , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinquan","family":"Li","sequence":"additional","affiliation":[{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University National Key Laboratory of Agricultural Microbiology, , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"College of Food Science and Technology, Huazhong Agricultural University Hubei Hongshan Laboratory, , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"College of Veterinary Medicine, Huazhong Agricultural University , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Buxin Road No. 97, Shenzhen 518000, China"},{"name":"Shenzhen Institute of Quality & Safety Inspection and Research , Buxin Road No. 97, Shenzhen 518000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Runze","family":"Li","sequence":"additional","affiliation":[{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University National Key Laboratory of Agricultural Microbiology, , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"College of Food Science and Technology, Huazhong Agricultural University Hubei Hongshan Laboratory, , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geng","family":"Zou","sequence":"additional","affiliation":[{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University National Key Laboratory of Agricultural Microbiology, , Shizishan Street No. 1, Wuhan 430070, China"},{"name":"College of Food Science and Technology, Huazhong Agricultural University Hubei Hongshan Laboratory, , Shizishan Street No. 1, Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,3,26]]},"reference":[{"key":"2024062912270168900_R1","article-title":"Tackling drug-resistant infections globally: final report and 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perspective","volume":"13","author":"Kalpana","year":"2023","journal-title":"Diagnostics"},{"key":"2024062912270168900_R5","article-title":"Antimicrobial peptides: mechanism of action, activity and clinical potential","volume":"8","author":"Zhang","year":"2021","journal-title":"Mil. Med. Res."},{"key":"2024062912270168900_R6","doi-asserted-by":"crossref","DOI":"10.1016\/j.tips.2019.04.012","article-title":"The vast structural diversity of antimicrobial peptides","volume":"40","author":"Koehbach","year":"2019","journal-title":"Trends Pharmacol. Sci."},{"key":"2024062912270168900_R7","doi-asserted-by":"crossref","DOI":"10.3390\/ijms20194877","article-title":"Non-lytic antibacterial peptides that translocate through bacterial membranes to act on intracellular targets","volume":"20","author":"Cardoso","year":"2019","journal-title":"Int. J. Mol. Sci."},{"key":"2024062912270168900_R8","doi-asserted-by":"crossref","DOI":"10.3390\/ijms232214151","article-title":"Activity and synergy of Cu-ATCUN antimicrobial peptides","volume":"23","author":"Greve","year":"2022","journal-title":"Int. J. Mol. 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Microbiol."},{"key":"2024062912270168900_R13","doi-asserted-by":"crossref","first-page":"2671","DOI":"10.1128\/AAC.02972-15","article-title":"Novel engineered peptides of a phage lysin as effective antimicrobials against multidrug-resistant Acinetobacter baumannii","volume":"60","author":"Thandar","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"2024062912270168900_R14","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1016\/j.omtn.2020.05.006","article-title":"Deep-AmPEP30: improve short antimicrobial peptides prediction with deep learning","volume":"20","author":"Yan","year":"2020","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2024062912270168900_R15","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1038\/s41587-022-01226-0","article-title":"Identification of antimicrobial peptides from the human gut microbiome using deep learning","volume":"40","author":"Ma","year":"2022","journal-title":"Nat. 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