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Reliable prediction of antibody, or B-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. A correlation between antigenicity, solvent accessibility, and flexibility in proteins was demonstrated. Subsequently, Thornton and colleagues proposed a method for identifying continuous epitopes in the protein(More)
Prediction of which peptides can bind major histocompatibility complex (MHC) molecules is commonly used to assist in the identification of T cell epitopes. However, because of the large numbers of different MHC molecules of interest, each associated with different predictive tools, tool generation and evaluation can be a very resource intensive task. A(More)
Over the last twenty years, the amount of information related to epitopes recognized in the course of T and B cell-mediated immune responses has dramatically increased. As of June 2004, a PubMed search using the word " epitope " , reveals a total of 5,173 records prior (with a large fraction of the 2004 records still to come). Epitope-based techniques are(More)
A B-cell epitope is the three-dimensional structure within an antigen that can be bound to the variable region of an antibody. The prediction of B-cell epitopes is highly desirable for various immunological applications, but has presented a set of unique challenges to the bioinformatics and immunology communities. Improving the accuracy of B-cell epitope(More)
Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide binding preference, which can be captured in prediction algorithms, allowing for the rapid scan of entire pathogen proteomes for peptide likely to bind MHC. Here(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 value of predictive algorithms for identifying CD8+ T (T(CD8+))-cell epitopes has not been adequately tested experimentally. Here we demonstrate that conventional bioinformatic methods predict the vast majority of T(CD8+)-cell epitopes derived from vaccinia virus WR strain (VACV-WR) in the H-2(b) mouse model. This approach reveals the breadth of T-cell(More)
The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), recently awarded 14 contracts to fund the Large-Scale Antibody and T Cell Epitope Discovery Program. This initiative is designed to identify immune epitopes from selected infectious agents utilizing complementary methods for epitope discovery.(More)
The Immune Epitope Database and Analysis Resources (IEDB) (www.immuneepitope.org) was recently developed to capture epitope related data. IEDB also hosts various bioinformatics tools that can be used to identify novel epitopes as well as to analyze and visualize existing epitope data. Herein, a comprehensive analysis was undertaken (i) to compile and(More)
The SIV-infected Indian rhesus macaque is the most established model of HIV infection, providing insight into pathogenesis and a system for testing novel vaccines. However, only a limited amount of information is available regarding the peptide-binding motifs and epitopes bound by their class I and class II MHC molecules. In this study, we utilized a(More)