title: Epitope scanning using virtual matrix-based algorithms.
abstract: Protein sequence and expression databases (transcriptomes) contain the information required to identify epitopes capable of generating protective immune responses in humans. A key event in the initiation of an immune response against disease is the presentation of antigenic peptide epitopes to T cells by human leukocyte antigen (HLA) molecules. Computational filtering tools that allow the prediction of HLA/epitope interaction can be applied to sequence databases to select for candidate epitopes, thus minimising the subsequent amount of laboratory work. Here, the basic principles of epitope prediction and a summary of the available prediction approaches are presented, with a particular emphasis on the use of algorithms based on virtual HLA-II quantitative matrices, capable of predicting promiscuous HLA-II ligands.
authors.affiliation: Department of Genomics and Information Sciences, Hoffmann-La Roche, Nutley, NJ 07110, USA. laura.raddrizzani@roche.com
authors.forename: L
authors.initials: L
authors.lastname: Raddrizzani
authors.forename: J
authors.initials: J
authors.lastname: Hammer
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D017951:Antigen Presentation; D019295:Computational Biology; D016208:Databases, Factual; D000939:Epitopes / Q000235:genetics* / Q000378:metabolism; D006680:HLA Antigens / Q000378:metabolism; D006801:Humans; D020407:Internet; D008969:Molecular Sequence Data; D011506:Proteins / Q000235:genetics / Q000276:immunology; D016415:Sequence Alignment / Q000706:statistics & numerical data; D012984:Software; D013601:T-Lymphocytes / Q000276:immunology; D014584:User-Computer Interface
chemical_list: D000939:Epitopes; D006680:HLA Antigens; D011506:Proteins