Combining computer algorithms with experimental approaches permits the rapid and accurate identification of T cell epitopes from defined antigens

J Immunol Methods. 2001 Nov 1;257(1-2):1-16. doi: 10.1016/s0022-1759(01)00459-8.


The identification of T cell epitopes from immunologically relevant antigens remains a critical step in the development of vaccines and methods for monitoring of T cell responses. This review presents an overview of strategies that employ computer algorithms for the selection of candidate peptides from defined proteins and subsequent verification of their in vivo relevance by experimental approaches. Several computer algorithms are currently being used for epitope prediction of various major histocompatibility complex (MHC) class I and II molecules, based either on the analysis of natural MHC ligands or on the binding properties of synthetic peptides. Moreover, the analysis of proteasomal digests of peptides and whole proteins has led to the development of algorithms for the prediction of proteasomal cleavages. In order to verify the generation of the predicted peptides during antigen processing in vivo as well as their immunogenic potential, several experimental approaches have been pursued in the recent past. Mass spectrometry-based bioanalytical approaches have been used specifically to detect predicted peptides among isolated natural ligands. Other strategies employ various methods for the stimulation of primary T cell responses against the predicted peptides and subsequent testing of the recognition pattern towards target cells that express the antigen.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Antigen Presentation
  • Cytokines / biosynthesis
  • Cytokines / genetics
  • Epitopes / chemistry*
  • Epitopes / genetics
  • Histocompatibility Antigens Class I / chemistry
  • Histocompatibility Antigens Class I / genetics
  • Histocompatibility Antigens Class II / chemistry
  • Histocompatibility Antigens Class II / genetics
  • Immunologic Techniques*
  • Molecular Sequence Data
  • RNA, Messenger / biosynthesis
  • RNA, Messenger / genetics
  • T-Lymphocytes / immunology*


  • Cytokines
  • Epitopes
  • Histocompatibility Antigens Class I
  • Histocompatibility Antigens Class II
  • RNA, Messenger