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TAPPred Prediction of TAP-Binding Peptides in Antigens

  • Manoj Bhasin
  • Sneh Lata
  • G.P.S. Raghava
Part of the Methods in Molecular Biology™ book series (MIMB, volume 409)

Summary

The transporter associated with antigen processing (TAP) plays a crucial role in the transport of the peptide fragments of the proteolysed antigenic or self-altered proteins to the endoplasmic reticulum where the association between these peptides and the major histocompatibility complex (MHC) class I molecules takes place. Therefore, prediction of TAP-binding peptides is highly helpful in identifying the MHC class I-restricted T-cell epitopes and hence in the subunit vaccine designing. In this chapter, we describe a support vector machine (SVM)-based method TAPPred that allows users to predict TAP-binding affinity of peptides over web. The server allows user to predict TAP binders using a simple SVM model or cascade SVM model. The server also allows user to customize the display/output. It is freely available for academicians and noncommercial organization at the address http://www.imtech.res.in/raghava/tappred.

Key Words

TAP MHC class I T-cell epitopes subunit vaccine SVM cascade SVM 

Notes

Acknowledgments

We acknowledge the financial support from the Council of Scientific and Industrial Research (CSIR) and Department of Biotechnology (DBT), Government of India.

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Manoj Bhasin
    • 1
  • Sneh Lata
    • 1
  • G.P.S. Raghava
    • 1
    • 2
  1. 1.Institute of Microbial TechnologyChandigarhIndia
  2. 2.UAMS, BRCIILittle Rock

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