Computational methods for prediction of T-cell epitopes--a framework for modelling, testing, and applications.
Computational models complement laboratory experimentation for efficient identification of MHC-binding peptides and T-cell epitopes. Methods for prediction of MHC-binding peptides include binding motifs, quantitative matrices, artificial neural networks, hidden Markov models, and molecular modelling. Models derived by these methods have been successfully used for prediction of T-cell epitopes in cancer, autoimmunity, infectious disease, and allergy. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures and performed according to strict standards. This requires careful selection of data for model building, and adequate testing and validation. A range of web-based databases and MHC-binding prediction programs are available. Although some available prediction programs for particular MHC alleles have reasonable accuracy, there is no guarantee that all models produce good quality predictions. In this article, we present and discuss a framework for modelling, testing, and applications of computational methods used in predictions of T-cell epitopes.
Brusic
Vladimir
V
Laboratories for Information Technology, 21 Heng Mui Keng Terrace, 119613, Singapore. vladimir@i2r.a-star.edu.sg
Bajic
Vladimir B
VB
Petrovsky
Nikolai
N
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D018984:Epitopes, T-Lymphocyte / Q000276:immunology* / Q000378:metabolism; D006801:Humans; D018448:Models, Immunological; D010446:Peptide Fragments / Q000276:immunology / Q000378:metabolism; D011485:Protein Binding / Q000276:immunology
D018984:Epitopes, T-Lymphocyte; D010446:Peptide Fragments