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There are two types of proteasomes, the constitutive form, expressed in most cell types, and the immunoproteasome, which is constitutively expressed in mature dendritic cells. Protective CD8 T cell epitopes are likely generated by the immunoproteasome and the constitutive proteasome, and here we have modeled and analyzed the cleavage by these two proteases.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have modeled the immunoproteasome and proteasome cleavage sites upon two non-overlapping sets of peptides consisting of 553 CD8 T cell epitopes, naturally processed and restricted by human MHCI molecules, and 382 peptides eluted from human MHCI molecules, respectively, using <jats:italic>N-grams<\/jats:italic>. Cleavage models were generated considering different epitope and MHCI-eluted fragment lengths and the same number of C-terminal flanking residues. Models were evaluated in 5-fold cross-validation. Judging by the Mathew's Correlation Coefficient (<jats:italic>MCC<\/jats:italic>), optimal cleavage models for the proteasome (<jats:italic>MCC<\/jats:italic> = 0.43 \u00b1 0.07) and the immunoproteasome (<jats:italic>MCC<\/jats:italic> = 0.36 \u00b1 0.06) were obtained from 12-residue peptide fragments. Using an independent dataset consisting of 137 HIV1-specific CD8 T cell epitopes, the immunoproteasome and proteasome cleavage models achieved <jats:italic>MCC<\/jats:italic> values of 0.30 and 0.18, respectively, comparatively better than those achieved by related methods. Using ROC analyses, we have also shown that, combined with MHCI-peptide binding predictions, cleavage predictions by the immunoproteasome and proteasome models significantly increase the discovery rate of CD8 T cell epitopes restricted by different MHCI molecules, including A*0201, A*0301, A*2402, B*0702, B*2705.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We have developed models that are specific to predict cleavage by the proteasome and the immunoproteasome. These models ought to be instrumental to identify protective CD8 T cell epitopes and are readily available for free public use at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/imed.med.ucm.es\/Tools\/PCPS\/\" ext-link-type=\"uri\">http:\/\/imed.med.ucm.es\/Tools\/PCPS\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-479","type":"journal-article","created":{"date-parts":[[2010,9,23]],"date-time":"2010-09-23T18:26:56Z","timestamp":1285266416000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":45,"title":["Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome"],"prefix":"10.1186","volume":"11","author":[{"given":"Carmen M","family":"Diez-Rivero","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esther M","family":"Lafuente","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro A","family":"Reche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2010,9,23]]},"reference":[{"key":"3936_CR1","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1146\/annurev.immunol.17.1.369","volume":"17","author":"KC Garcia","year":"1999","unstructured":"Garcia KC, Teyton L, Wilson IA: Structural basis of T cell recognition. 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