{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:39:04Z","timestamp":1740184744927,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,2,2]],"date-time":"2018-02-02T00:00:00Z","timestamp":1517529600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000050","name":"National Heart, Lung and Blood Institute","doi-asserted-by":"crossref","award":["ZO1-HL-001285"],"award-info":[{"award-number":["ZO1-HL-001285"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Rachadapisek Sompot Fund for Postdoctoral Fellowship"},{"DOI":"10.13039\/501100002873","name":"Chulalongkorn University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002873","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present AbDesigner3D, a new tool for identification of optimal immunizing peptides for antibody production using a peptide-based strategy. AbDesigner3D integrates 3D structural data from the Protein Data Bank (PDB) with UniProt data, which includes basic sequence data, post-translational modification sites, SNP occurrences and more. Other features, such as uniqueness and conservation scores, are calculated based on sequences from UniProt. The 3D visualization capabilities allow an intuitive interface, while an abundance of quantitative output simplifies the process of comparing immunogen peptides. Important quantitative features added in this tool include calculation and display of accessible surface area (ASA) and protein-protein interacting residues (PPIR). The specialized data visualization features of AbDesigner3D will greatly assist users to optimize their choice of immunizing peptides.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>AbDesigner3D is freely available at http:\/\/sysbio.chula.ac.th\/AbDesigner3D or https:\/\/hpcwebapps.cit.nih.gov\/AbDesigner3D\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty055","type":"journal-article","created":{"date-parts":[[2018,1,31]],"date-time":"2018-01-31T18:56:35Z","timestamp":1517424995000},"page":"2158-2160","source":"Crossref","is-referenced-by-count":3,"title":["AbDesigner3D: a structure-guided tool for peptide-based antibody production"],"prefix":"10.1093","volume":"34","author":[{"given":"Thammakorn","family":"Saethang","sequence":"first","affiliation":[{"name":"Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"}]},{"given":"Kenneth","family":"Hodge","sequence":"additional","affiliation":[{"name":"Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"}]},{"given":"Ingorn","family":"Kimkong","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand"}]},{"given":"D Michael","family":"Payne","sequence":"additional","affiliation":[{"name":"Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"}]},{"given":"Mark A","family":"Knepper","sequence":"additional","affiliation":[{"name":"Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, USA"}]},{"given":"Trairak","family":"Pisitkun","sequence":"additional","affiliation":[{"name":"Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"},{"name":"Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,2,2]]},"reference":[{"key":"2023012713411438800_bty055-B1","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/nrd.2016.268","article-title":"Strategies and challenges for the next generation of antibody-drug conjugates","volume":"16","author":"Beck","year":"2017","journal-title":"Nat. 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