Structural Immunoinformatics: Understanding MHC-Peptide-TR Binding

  • Javed Mohammed Khan
  • Joo Chuan Tong
  • Shoba Ranganathan
Part of the Immunomics Reviews: book series (IMMUN, volume 3)


Adaptive immune responses are governed by major histocompatibility complexes (MHC) binding to specific short antigenic peptides and then this peptide bound major histocompatibility complex (pMHC) being recognized by the T cell receptor (TR) which activates the T cells. The use of critical sequence-structure-function information to understand the principles underlying MHC specific peptide binding is well established and the focus is now on understanding TR recognition of pMHC complexes. Three-dimensional X-ray structures of pMHC complexes bound to the TR that are today characterized in good numbers facilitate structural analysis further. It is thus possible to predict potential T cell epitopes for vaccine design by utilizing information derived from available experimental structures which offer an alternative to sequence-based approaches that require large dataset for training. In this chapter, we introduce the use of structural data, a comparative modeling and docking protocol for epitope prediction for specific MHC alleles and also compare the results of our experiments on different disease-specific alleles. We also talk about the possibilities of predicting how well a pMHC complex can bind to the TR.


Major Histocompatibility Complex Human Leukocyte Antigen Major Histocompatibility Complex Class Human Leukocyte Antigen Class Major Histocompatibility Complex Molecule 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Javed Mohammed Khan
  • Joo Chuan Tong
  • Shoba Ranganathan
    • 1
  1. 1.Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in BioinformaticsMacquarie UniversitySydneyAustralia

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