{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T12:45:44Z","timestamp":1772196344799,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: T-cell epitope identification is a critical immunoinformatic problem within vaccine design. To be an epitope, a peptide must bind an MHC protein.<\/jats:p>\n               <jats:p>Results: Here, we present EpiTOP, the first server predicting MHC class II binding based on proteochemometrics, a QSAR approach for ligands binding to several related proteins. EpiTOP uses a quantitative matrix to predict binding to 12 HLA-DRB1 alleles. It identifies 89% of known epitopes within the top 20% of predicted binders, reducing laboratory labour, materials and time by 80%. EpiTOP is easy to use, gives comprehensive quantitative predictions and will be expanded and updated with new quantitative matrices over time.<\/jats:p>\n               <jats:p>Availability: EpiTOP is freely accessible at http:\/\/www.pharmfac.net\/EpiTOP<\/jats:p>\n               <jats:p>Contact: \u00a0idoytchinova@pharmfac.net<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq324","type":"journal-article","created":{"date-parts":[[2010,6,25]],"date-time":"2010-06-25T00:19:35Z","timestamp":1277425175000},"page":"2066-2068","source":"Crossref","is-referenced-by-count":62,"title":["EpiTOP\u2014a proteochemometric tool for MHC class II binding prediction"],"prefix":"10.1093","volume":"26","author":[{"given":"Ivan","family":"Dimitrov","sequence":"first","affiliation":[{"name":"1 Faculty of Pharmacy, Medical University of Sofia, 2 Dunav st, 1000 Sofia, Bulgaria and 2Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK"}]},{"given":"Panayot","family":"Garnev","sequence":"additional","affiliation":[{"name":"1 Faculty of Pharmacy, Medical University of Sofia, 2 Dunav st, 1000 Sofia, Bulgaria and 2Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK"}]},{"given":"Darren R.","family":"Flower","sequence":"additional","affiliation":[{"name":"1 Faculty of Pharmacy, Medical University of Sofia, 2 Dunav st, 1000 Sofia, Bulgaria and 2Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK"}]},{"given":"Irini","family":"Doytchinova","sequence":"additional","affiliation":[{"name":"1 Faculty of Pharmacy, Medical University of Sofia, 2 Dunav st, 1000 Sofia, Bulgaria and 2Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK"}]}],"member":"286","published-online":{"date-parts":[[2010,6,23]]},"reference":[{"key":"2023012508033643600_B1","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1016\/S0031-3203(96)00142-2","article-title":"The use of the area under the ROC curve in the evaluation of machine learning algorithms","volume":"30","author":"Bradley","year":"1997","journal-title":"Pattern Recognition"},{"key":"2023012508033643600_B2","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1007\/s00251-005-0798-y","article-title":"Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications","volume":"57","author":"Bui","year":"2005","journal-title":"Immunogenetics"},{"key":"2023012508033643600_B3","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/j.ejmech.2009.09.049","article-title":"Peptide binding to the HLA-DRB1 supertype: a proteochemometrics analysis","volume":"45","author":"Dimitrov","year":"2010","journal-title":"Eur. 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An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction","volume":"10","author":"Nielsen","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012508033643600_B13","doi-asserted-by":"crossref","first-page":"e91","DOI":"10.1371\/journal.pbio.0030091","article-title":"The immune epitope database and analysis resource: from vision to blueprint","volume":"3","author":"Peters","year":"2005","journal-title":"PLoS Biol."},{"key":"2023012508033643600_B14","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1007\/s00251-004-0709-7","article-title":"Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles","volume":"56","author":"Reche","year":"2004","journal-title":"Immunogenetics"},{"key":"2023012508033643600_B15","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/17.12.1236","article-title":"ProPred: prediction of HLA-DR binding sites","volume":"17","author":"Singh","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012508033643600_B16","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/9858","article-title":"Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices","volume":"17","author":"Sturniolo","year":"1999","journal-title":"Nat. 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