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Here, the sequences of ten cysteine proteases of types A, B and C of Leishmania major were obtained from GeneDB database. Prediction of MHC class I epitopes of these cysteine proteases was performed by NetCTL program version 1.2. In addition, by using BcePred server, different structural properties of the proteins were predicted to find out their potential B cell epitopes. According to this computational analysis, nine regions were predicted as B cell epitopes. The results provide useful information for designing peptide-based vaccines.<\/jats:p>","DOI":"10.1016\/s1672-0229(08)60037-6","type":"journal-article","created":{"date-parts":[[2009,11,28]],"date-time":"2009-11-28T02:52:42Z","timestamp":1259376762000},"page":"87-95","source":"Crossref","is-referenced-by-count":8,"title":["Computational Analysis of Cysteine Proteases (Clan CA, Family C1) of <i>Leishmania Major<\/i> to Find Potential Epitopic Regions"],"prefix":"10.1093","volume":"7","author":[{"given":"Babak","family":"Saffari","sequence":"first","affiliation":[{"name":"Department of Biology, College of Sciences, Shiraz University , Shiraz , Iran"}]},{"given":"Hassan","family":"Mohabatkar","sequence":"additional","affiliation":[{"name":"Department of Biology, College of Sciences, Shiraz University , Shiraz , Iran"}]}],"member":"286","published-online":{"date-parts":[[2009,11,25]]},"reference":[{"key":"2024051008262480500_bib1","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1006\/expr.1994.1084","article-title":"The developmental biology of Leishmania promastigotes","volume":"79","author":"Bates","year":"1994","journal-title":"Exp. 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Immunol."},{"key":"2024051008262480500_bib10","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1002\/eji.1830250435","article-title":"Antigen presentation by Leishmania mexicana-infected macrophages: activation of helper T cells specific for amastigote cysteine proteases requires intracellular killing of the parasites","volume":"25","author":"Wolfram","year":"1995","journal-title":"Eur. J. Immunol."},{"key":"2024051008262480500_bib11","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1128\/iai.63.9.3559-3566.1995","article-title":"Leishmania pifanoi amastigote antigens protect mice against cutaneous leishmaniasis","volume":"63","author":"Soong","year":"1995","journal-title":"Infect. 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Virol."},{"key":"2024051008262480500_bib44","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/0165-2478(93)90072-A","article-title":"Correlation between the location of antigenic sites and the prediction of turns in proteins","volume":"36","author":"Pellequer","year":"1993","journal-title":"Immunol. Lett."},{"key":"2024051008262480500_bib45","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/0014-5793(90)80535-Q","article-title":"A semi-empirical method for prediction of antigenic determinants on protein antigens","volume":"276","author":"Kolaskar","year":"1990","journal-title":"FEBS Lett."},{"key":"2024051008262480500_bib46","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/0022-2836(78)90408-4","article-title":"Conformation of amino acid side-chains in proteins","volume":"125","author":"Janin","year":"1978","journal-title":"J. Mol. 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