{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T20:04:22Z","timestamp":1787169862838,"version":"3.56.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2018,7,6]],"date-time":"2018-07-06T00:00:00Z","timestamp":1530835200000},"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 R&D Program of China","doi-asserted-by":"crossref","award":["2016YFC1305800"],"award-info":[{"award-number":["2016YFC1305800"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2016YFC1305805"],"award-info":[{"award-number":["2016YFC1305805"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31670724"],"award-info":[{"award-number":["31670724"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003397","name":"Huazhong University of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003397","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>A structural database of peptide\u2013protein interactions is important for drug discovery targeting peptide-mediated interactions. Although some peptide databases, especially for special types of peptides, have been developed, a comprehensive database of cleaned peptide\u2013protein complex structures is still not available. Such cleaned structures are valuable for docking and scoring studies in structure-based drug design. Here, we have developed PepBDB\u2014a curated Peptide Binding DataBase of biological complex structures from the Protein Data Bank (PDB). PepBDB presents not only cleaned structures but also extensive information about biological peptide\u2013protein interactions, and allows users to search the database with a variety of options and interactively visualize the search results.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PepBDB is available at http:\/\/huanglab.phys.hust.edu.cn\/pepbdb\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty579","type":"journal-article","created":{"date-parts":[[2018,7,4]],"date-time":"2018-07-04T15:39:34Z","timestamp":1530718774000},"page":"175-177","source":"Crossref","is-referenced-by-count":87,"title":["PepBDB: a comprehensive structural database of biological peptide\u2013protein interactions"],"prefix":"10.1093","volume":"35","author":[{"given":"Zeyu","family":"Wen","sequence":"first","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiahua","family":"He","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huanyu","family":"Tao","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheng-You","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,7,6]]},"reference":[{"key":"2023013107214810000_bty579-B1","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":"2023013107214810000_bty579-B2","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.gpb.2013.03.002","article-title":"PepBind: a comprehensive database and computational tool for analysis of protein\u2013peptide interactions","volume":"11","author":"Das","year":"2013","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2023013107214810000_bty579-B3","doi-asserted-by":"crossref","first-page":"W361","DOI":"10.1093\/nar\/gkx335","article-title":"The pepATTRACT web server for blind, large-scale peptide\u2013protein docking","volume":"45","author":"de Vries","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023013107214810000_bty579-B4","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1002\/ijch.201300024","article-title":"JSmol and the next-generation web-based representation of 3D molecular structure as applied to Proteopedia","volume":"53","author":"Hanson","year":"2013","journal-title":"Isreal J. Chem"},{"key":"2023013107214810000_bty579-B5","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1002\/prot.21949","article-title":"An iterative knowledge-based scoring function for protein\u2013protein recognition","volume":"72","author":"Huang","year":"2008","journal-title":"Proteins"},{"key":"2023013107214810000_bty579-B6","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1021\/ci200227u","article-title":"LigPlot+: multiple ligand? CProtein interaction diagrams for drug discovery","volume":"51","author":"Laskowski","year":"2011","journal-title":"J. Chem. Inf. 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Biotechnol"},{"key":"2023013107214810000_bty579-B9","first-page":"2444","article-title":"Improved tools for biological sequence comparison","volume":"85","author":"Pearson","year":"1988","journal-title":"Biochemistry"},{"key":"2023013107214810000_bty579-B10","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.copbio.2008.06.004","article-title":"Peptide-mediated interactions in biological systems: new discoveries and applications","volume":"19","author":"Petsalaki","year":"2008","journal-title":"Curr. Opin. 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