{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T14:36:03Z","timestamp":1774622163146,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T00:00:00Z","timestamp":1736380800000},"content-version":"vor","delay-in-days":48,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32200529"],"award-info":[{"award-number":["32200529"]}],"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":["82304351"],"award-info":[{"award-number":["82304351"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The unique cyclic structure of cyclic peptides grants them remarkable stability and bioactivity, making them powerful candidates for treating various diseases. However, the lack of standardized tools for cyclic peptide data has hindered their potential in today\u2019s artificial intelligence\u2013driven efficient drug design landscape. To bridge this gap, here we introduce a Python package named cyclicpeptide specifically for cyclic peptide drug design. This package provides standardized tools such as Structure2Sequence, Sequence2Structure, and format transformation to process, convert, and standardize cyclic peptide structure and sequence data. Additionally, it includes GraphAlignment for cyclic peptide\u2013specific alignment and search and PropertyAnalysis to enhance the understanding of their drug-like properties and potential applications. This comprehensive suite of tools aims to streamline the integration of cyclic peptides into modern drug discovery pipelines, accelerating the development of cyclic peptide\u2013based therapeutics.<\/jats:p>","DOI":"10.1093\/bib\/bbae714","type":"journal-article","created":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T11:32:31Z","timestamp":1736422351000},"source":"Crossref","is-referenced-by-count":6,"title":["<i>cyclicpeptide<\/i>: a Python package for cyclic peptide drug design"],"prefix":"10.1093","volume":"26","author":[{"given":"Liu","family":"Yang","sequence":"first","affiliation":[{"name":"National Center, Children\u2019s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , 3333 Binsheng Road, Hangzhou 310052 ,","place":["P. R. China"]}]},{"given":"Suqi","family":"Cao","sequence":"additional","affiliation":[{"name":"National Center, Children\u2019s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , 3333 Binsheng Road, Hangzhou 310052 ,","place":["P. R. China"]}]},{"given":"Lei","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, Shanghai Tenth People\u2019s Hospital, School of Life Sciences and Technology, Tongji University , 1239 Siping Road, Shanghai 200072 ,","place":["P. R. China"]}]},{"given":"Ruixin","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, Shanghai Tenth People\u2019s Hospital, School of Life Sciences and Technology, Tongji University , 1239 Siping Road, Shanghai 200072 ,","place":["P. R. China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9287-122X","authenticated-orcid":false,"given":"Dingfeng","family":"Wu","sequence":"additional","affiliation":[{"name":"National Center, Children\u2019s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , 3333 Binsheng Road, Hangzhou 310052 ,","place":["P. R. China"]}]}],"member":"286","published-online":{"date-parts":[[2025,1,9]]},"reference":[{"key":"2025010911320466000_ref1","doi-asserted-by":"publisher","first-page":"11913","DOI":"10.1021\/acs.jmedchem.2c01077","article-title":"Cyclic peptide screening methods for preclinical drug discovery","volume":"65","author":"Li","year":"2022","journal-title":"J Med Chem"},{"key":"2025010911320466000_ref2","doi-asserted-by":"publisher","first-page":"1158","DOI":"10.1038\/s41589-023-01373-8","article-title":"An anti-biofilm cyclic peptide targets a secreted aminopeptidase from P. 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