{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T10:33:37Z","timestamp":1758710017834},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"suppl_1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2004,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Processing and presentation of major histocompatibility complex class I antigens to cytotoxic T-lymphocytes is crucial for immune surveillance against intracellular bacteria, parasites, viruses and tumors. Identification of antigenic regions on pathogen proteins will play a pivotal role in designer vaccine immunotherapy. We have developed a system that not only identifies high binding T-cell antigenic epitopes, but also class I T-cell antigenic clusters termed immunological hot spots.<\/jats:p>\n               <jats:p>Methods: MULTIPRED, a computational system for promiscuous prediction of HLA class I binders, uses artificial neural networks (ANN) and hidden Markov models (HMM) as predictive engines. The models were rigorously trained, tested and validated using experimentally identified HLA class I T-cell epitopes from human melanoma related proteins and human papillomavirus proteins E6 and E7. We have developed a scoring scheme for identification of immunological hot spots for HLA class I molecules, which is the sum of the highest four predictions within a window of 30 amino acids.<\/jats:p>\n               <jats:p>Results: Our predictions against experimental data from four melanoma-related proteins showed that MULTIPRED ANN and HMM models could predict T-cell epitopes with high accuracy. The analysis of proteins E6 and E7 showed that ANN models appear to be more accurate for prediction of HLA-A3 hot spots and HMM models for HLA-A2 predictions. For illustration of its utility we applied MULTIPRED for prediction of promiscuous T-cell epitopes in all four SARS coronavirus structural proteins. MULTIPRED predicted HLA-A2 and HLA-A3 hot spots in each of these proteins.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth943","type":"journal-article","created":{"date-parts":[[2004,7,19]],"date-time":"2004-07-19T17:07:37Z","timestamp":1090256857000},"page":"i297-i302","source":"Crossref","is-referenced-by-count":22,"title":["Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens"],"prefix":"10.1093","volume":"20","author":[{"given":"K.N.","family":"Srinivasan","sequence":"first","affiliation":[]},{"given":"G.L.","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"A.M.","family":"Khan","sequence":"additional","affiliation":[]},{"given":"J.T.","family":"August","sequence":"additional","affiliation":[]},{"given":"V.","family":"Brusic","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,8,4]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/suppl_1\/i297\/218059","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/suppl_1\/i297\/218059","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,3]],"date-time":"2023-07-03T05:38:51Z","timestamp":1688362731000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/suppl_1\/i297\/218059"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,8,4]]},"references-count":0,"journal-issue":{"issue":"suppl_1","published-print":{"date-parts":[[2004,8,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth943","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2004,8,4]]},"published":{"date-parts":[[2004,8,4]]}}}