UNLABELLED The National Agricultural Biotechnology Information Center (NABIC) reconstructed an AllergenPro database for allergenic proteins analysis and allergenicity prediction. The AllergenPro is an integrated web-based system providing information about allergen in foods, microorganisms, animals and plants. The allergen database has the three main features namely, (1) allergen list with epit...

Prediction methods for identifying binding peptides could minimize the number of peptides required to be synthesized and assayed, and thereby facilitate the identification of potential T-cell epitopes. We developed a bioinformatics method for the prediction of peptide binding to T-cell molecules. The major T-cell contributors are selected for the dataset preparation due to its availability and ...

UNLABELLED The HMMTOP transmembrane topology prediction server predicts both the localization of helical transmembrane segments and the topology of transmembrane proteins. Recently, several improvements have been introduced to the original method. Now, the user is allowed to submit additional information about segment localization to enhance the prediction power. This option improves the predic...

One of the major challenges in the field of vaccine design is to identify the B-cell epitopes in ever-evolving viruses. Various prediction servers have been developed to predict linear or conformational epitopes, each relying on different physicochemical properties and adopting distinct search strategies. We propose meta learning approaches to epitope prediction based on stacked generalization ...

CD8+ T cells are key effectors of the immune response against human cytomegalovirus (HCMV). A number of HCMV-derived CD8+ T cell epitopes are known. Using epitope prediction and subsequent testing for interferon-gamma responses by the ELISPOT assay, we identified an optimal human leukocyte antigen (HLA)-A*0201-restricted CD8+ T cell epitope derived from the major immediate early 1 (IE-1) gene p...

Summary: Antibody epitope mapping is a key step in understanding antibody–antigen recognition and is of particular interest for drug development, diagnostics and vaccine design. Most computational methods for epitope prediction are based on properties of the antigen sequence and/or structure, not taking into account the antibody for which the epitope is predicted. Here, we introduce PEASE, a we...

Identifying protein surface regions preferentially recognizable by antibodies (antigenic epitopes) is at the heart of new immuno-diagnostic reagent discovery and vaccine design, and computational methods for antigenic epitope prediction provide crucial means to serve this purpose. Many linear B-cell epitope prediction methods were developed, such as BepiPred, ABCPred, AAP, BCPred, BayesB, BEOra...

In recent years, a lot of efforts have been made in conformational epitope prediction as antigen proteins usually bind antibodies with an assembly of sequentially discontinuous and structurally compact surface residues. Currently, only a few methods for spatial epitope prediction are available with focus on single residue propensity scales or continual segments clustering. In the method of SEPP...

BACKGROUND The 2009 pandemic influenza was milder than expected. Based on the apparent lack of pre-existing cross-protective antibodies to the A (H1N1)pdm09 strain, it was hypothesized that pre-existing CD4+ T cellular immunity provided the crucial immunity that led to an attenuation of disease severity. We carried out a pilot scale study by conducting in silico and in vitro T cellular assays i...