{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T21:33:57Z","timestamp":1782768837039,"version":"3.54.5"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HHSN272201200010C"],"award-info":[{"award-number":["HHSN272201200010C"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["75N93019C00001"],"award-info":[{"award-number":["75N93019C00001"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The Immune Epitope Database Analysis Resource (IEDB-AR, http:\/\/tools.iedb.org\/) is a companion website to the IEDB that provides computational tools focused on the prediction and analysis of B and T cell epitopes. All of the tools are freely available through the public website and many are also available through a REST API and\/or a downloadable command-line tool. A virtual machine image of the entire site is also freely available for non-commercial use and contains most of the tools on the public site. Here, we describe the tools and functionalities that are available in the IEDB-AR, focusing on the 10 new tools that have been added since the last report in the 2012 NAR webserver edition. In addition, many of the tools that were already hosted on the site in 2012 have received updates to newest versions, including NetMHC, NetMHCpan, BepiPred and DiscoTope. Overall, this IEDB-AR update provides a substantial set of updated and novel features for epitope prediction and analysis.<\/jats:p>","DOI":"10.1093\/nar\/gkz452","type":"journal-article","created":{"date-parts":[[2019,5,10]],"date-time":"2019-05-10T15:21:11Z","timestamp":1557501671000},"page":"W502-W506","source":"Crossref","is-referenced-by-count":389,"title":["IEDB-AR: immune epitope database\u2014analysis resource in 2019"],"prefix":"10.1093","volume":"47","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1381-7434","authenticated-orcid":false,"given":"Sandeep Kumar","family":"Dhanda","sequence":"first","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2136-1801","authenticated-orcid":false,"given":"Swapnil","family":"Mahajan","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sinu","family":"Paul","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Yan","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haeuk","family":"Kim","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin Closter","family":"Jespersen","sequence":"additional","affiliation":[{"name":"Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa","family":"Jurtz","sequence":"additional","affiliation":[{"name":"Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8036-2647","authenticated-orcid":false,"given":"Massimo","family":"Andreatta","sequence":"additional","affiliation":[{"name":"Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark"},{"name":"Instituto de Investigaciones Biotecnol\u00f3gicas, Universidad Nacional de San Mart\u00edn, Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason A","family":"Greenbaum","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2615-5695","authenticated-orcid":false,"given":"Paolo","family":"Marcatili","sequence":"additional","affiliation":[{"name":"Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessandro","family":"Sette","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"},{"name":"Department of Medicine, University of California, San Diego, CA 92122, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morten","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark"},{"name":"Instituto de Investigaciones Biotecnol\u00f3gicas, Universidad Nacional de San Mart\u00edn, Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bjoern","family":"Peters","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"},{"name":"Department of Medicine, University of California, San Diego, CA 92122, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,5,22]]},"reference":[{"key":"2019062808323993300_B1","doi-asserted-by":"crossref","first-page":"D339","DOI":"10.1093\/nar\/gky1006","article-title":"The Immune Epitope Database (IEDB): 2018 update","volume":"47","author":"Vita","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019062808323993300_B2","doi-asserted-by":"crossref","first-page":"278","DOI":"10.3389\/fimmu.2017.00278","article-title":"The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design","volume":"8","author":"Fleri","year":"2017","journal-title":"Front. Immunol."},{"key":"2019062808323993300_B3","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1111\/imm.12816","article-title":"Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity","volume":"153","author":"Dhanda","year":"2018","journal-title":"Immunology"},{"key":"2019062808323993300_B4","doi-asserted-by":"crossref","first-page":"W525","DOI":"10.1093\/nar\/gks438","article-title":"Immune epitope database analysis resource","volume":"40","author":"Kim","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2019062808323993300_B5","doi-asserted-by":"crossref","first-page":"18.19.11","DOI":"10.1002\/cpim.12","article-title":"TepiTool: a pipeline for computational prediction of T cell epitope candidates","volume":"114","author":"Paul","year":"2016","journal-title":"Curr. Protoc. Immunol."},{"key":"2019062808323993300_B6","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.jim.2013.10.003","article-title":"MHC-NP: predicting peptides naturally processed by the MHC","volume":"400\u2013401","author":"Giguere","year":"2013","journal-title":"J. Immunol. Methods"},{"key":"2019062808323993300_B7","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.3389\/fimmu.2018.01795","article-title":"Determination of a predictive cleavage motif for eluted major histocompatibility complex Class II ligands","volume":"9","author":"Paul","year":"2018","journal-title":"Front. Immunol."},{"key":"2019062808323993300_B8","doi-asserted-by":"crossref","first-page":"e1003266","DOI":"10.1371\/journal.pcbi.1003266","article-title":"Properties of MHC class I presented peptides that enhance immunogenicity","volume":"9","author":"Calis","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"2019062808323993300_B9","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.3389\/fimmu.2018.01369","article-title":"Predicting HLA CD4 immunogenicity in human populations","volume":"9","author":"Dhanda","year":"2018","journal-title":"Front. Immunol."},{"key":"2019062808323993300_B10","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1111\/jth.12634","article-title":"Recombinant factor VIIa analog in the management of hemophilia with inhibitors: results from a multicenter, randomized, controlled trial of vatreptacog alfa","volume":"12","author":"Lentz","year":"2014","journal-title":"J. Thromb. 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