title: A combination of epitope prediction and molecular docking allows for good identification of MHC class I restricted T-cell epitopes.
abstract: In silico identification of T-cell epitopes is emerging as a new methodology for the study of epitope-based vaccines against viruses and cancer. In order to improve accuracy of prediction, we designed a novel approach, using epitope prediction methods in combination with molecular docking techniques, to identify MHC class I restricted T-cell epitopes. Analysis of the HIV-1 p24 protein and influenza virus matrix protein revealed that the present approach is effective, yielding prediction accuracy of over 80% with respect to experimental data. Subsequently, we applied such a method for prediction of T-cell epitopes in SARS coronavirus (SARS-CoV) S, N and M proteins. Based on available experimental data, the prediction accuracy is up to 90% for S protein. We suggest the use of epitope prediction methods in combination with 3D structural modelling of peptide-MHC-TCR complex to identify MHC class I restricted T-cell epitopes for use in epitope based vaccines like HIV and human cancers, which should provide a valuable step forward for the design of better vaccines and may provide in depth understanding about activation of T-cell epitopes by MHC binding peptides.
authors.affiliation: College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China. snow_dance@sina.com
authors.forename: Xue Wu
authors.initials: XW
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry* / Q000276:immunology*; D016655:HIV Core Protein p24 / Q000737:chemistry / Q000276:immunology; D015395:Histocompatibility Antigens Class I / Q000737:chemistry / Q000276:immunology*; D006801:Humans; D062105:Molecular Docking Simulation; D013601:T-Lymphocytes / Q000737:chemistry* / Q000276:immunology*; D014763:Viral Matrix Proteins / Q000737:chemistry / Q000276:immunology
chemical_list: D018984:Epitopes, T-Lymphocyte; D016655:HIV Core Protein p24; D015395:Histocompatibility Antigens Class I; C488936:M1 protein, Influenza A virus; D014763:Viral Matrix Proteins