title: Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?
abstract: Prediction methods as well as experimental methods for T-cell epitope discovery have developed significantly in recent years. High-throughput experimental methods have made it possible to perform full-length protein scans for epitopes restricted to a limited number of MHC alleles. The high costs and limitations regarding the number of proteins and MHC alleles that are feasibly handled by such experimental methods have made in silico prediction models of high interest. MHC binding prediction methods are today of a very high quality and can predict MHC binding peptides with high accuracy. This is possible for a large range of MHC alleles and relevant length of binding peptides. The predictions can easily be performed for complete proteomes of any size. Prediction methods are still, however, dependent on good experimental methods for validation, and should merely be used as a guide for rational epitope discovery. We expect prediction methods as well as experimental validation methods to continue to develop and that we will soon see clinical trials of products whose development has been guided by prediction methods.
authors.affiliation: Technical University of Denmark-DTU, Center for Biological Sequence Analysis, Department of Systems Biology, Kemitorvet 208, DK 2800, Kgs. Lyngby, Denmark.
authors.forename: Claus
authors.initials: C
authors.lastname: Lundegaard
authors.forename: Ole
authors.initials: O
authors.lastname: Lund
authors.forename: Morten
authors.initials: M
authors.lastname: Nielsen
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018984:Epitopes, T-Lymphocyte / Q000276:immunology*; D057166:High-Throughput Screening Assays / Q000379:methods*; D015395:Histocompatibility Antigens Class I / Q000032:analysis; D000949:Histocompatibility Antigens Class II / Q000032:analysis; D006801:Humans; D008285:Major Histocompatibility Complex / Q000235:genetics / Q000502:physiology; D011485:Protein Binding / Q000276:immunology / Q000502:physiology; D012107:Research Design
chemical_list: D018984:Epitopes, T-Lymphocyte; D015395:Histocompatibility Antigens Class I; D000949:Histocompatibility Antigens Class II