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BACKGROUND MHC class II binding predictions are widely used to identify epitope candidates in infectious agents, allergens, cancer and autoantigens. The vast majority of prediction algorithms for human MHC class II to date have targeted HLA molecules encoded in the DR locus. This reflects a significant gap in knowledge as HLA DP and DQ molecules are(More)
The identification of MHC class II restricted peptide epitopes is an important goal in immunological research. A number of computational tools have been developed for this purpose, but there is a lack of large-scale systematic evaluation of their performance. Herein, we used a comprehensive dataset consisting of more than 10,000 previously unpublished(More)
We present a new release of the immune epitope database analysis resource (IEDB-AR, http://tools.immuneepitope.org), a repository of web-based tools for the prediction and analysis of immune epitopes. New functionalities have been added to most of the previously implemented tools, and a total of eight new tools were added, including two B-cell epitope(More)
The immune epitope database analysis resource (IEDB-AR: http://tools.iedb.org) is a collection of tools for prediction and analysis of molecular targets of T- and B-cell immune responses (i.e. epitopes). Since its last publication in the NAR webserver issue in 2008, a new generation of peptide:MHC binding and T-cell epitope predictive tools have been added.(More)
BACKGROUND The Immune Epitope Database contains information on immune epitopes curated manually from the scientific literature. Like similar projects in other knowledge domains, significant effort is spent on identifying which articles are relevant for this purpose. RESULTS We here report our experience in automating this process using Naïve Bayes(More)
Successful predictions of peptide MHC binding typically require a large set of binding data for the specific MHC molecule that is examined. Structure based prediction methods promise to circumvent this requirement by evaluating the physical contacts a peptide can make with an MHC molecule based on the highly conserved 3D structure of peptide:MHC complexes.(More)
Coxiella burnetii is an obligate intracellular gram-negative bacterium that causes acute Q fever and chronic infections in humans. A killed, whole cell vaccine is efficacious, but vaccination can result in severe local or systemic adverse reactions. Although T cell responses are considered pivotal for vaccine derived protective immunity, the epitope targets(More)
Hydrogen (H2), a new antioxidant, was reported to reduce (•)OH and ONOO(-) selectively and inhibit certain proinflammatory mediators to product, without disturbing metabolic redox reactions or ROS involved in cell signaling. We herein aim to explore its protective effects on acute renal injury in sodium taurocholate-induced acute pancreatitis and its(More)
Background: Major histocompatibility complex (MHC) class I molecules play key roles in host immunity against pathogens by presenting peptide antigens to CD8+ T-cells. Many variants of MHC molecules exist, and each has a unique preference for certain peptide ligands. Both experimental approaches and computational algorithms have been utilized to analyze(More)
Acute renal injury caused by acute necrotizing pancreatitis (ANP) is a common complication that is associated with a high rate of mortality. Paeoniflorin is the active ingredient of paeonia radix and exhibits a number of pharmacological effects, such as anti‑inflammatory, anticancer, analgesic and immunomodulatory effects. The present study detected the(More)