TepiTool: A Pipeline for Computational Prediction of T Cell Epitope Candidates

Sinu Paul1, John Sidney1, Alessandro Sette1, Bjoern Peters1

1 La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla
Publication Name:  Current Protocols in Immunology
Unit Number:  Unit 18.19
DOI:  10.1002/cpim.12
Online Posting Date:  August, 2016
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Abstract

Computational prediction of T cell epitope candidates is currently being used in several applications including vaccine discovery studies, development of diagnostics, and removal of unwanted immune responses against protein therapeutics. There have been continuous improvements in the performance of MHC binding prediction tools, but their general adoption by immunologists has been slow due to the lack of user‐friendly interfaces and guidelines. Current tools only provide minimal advice on what alleles to include, what lengths to consider, how to deal with homologous peptides, and what cutoffs should be considered relevant. This protocol provides step‐by‐step instructions with necessary recommendations for prediction of the best T cell epitope candidates with the newly developed online tool called TepiTool. TepiTool, which is part of the Immune Epitope Database (IEDB), provides some of the top MHC binding prediction algorithms for number of species including humans, chimpanzees, bovines, gorillas, macaques, mice, and pigs. The TepiTool is freely accessible at http://tools.iedb.org/tepitool/. © 2016 by John Wiley & Sons, Inc.

Keywords: binding affinity prediction; CTL epitope prediction; MHC class I; MHC class II; T cell epitope

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Computational Prediction of Peptides Binding to MHC Class I and Class II Molecules
  • Commentary
  • Figures
     
 
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Materials

Basic Protocol 1: Computational Prediction of Peptides Binding to MHC Class I and Class II Molecules

  Materials
  • Computer with Internet browser and proper Internet connection
  • Protein sequence(s) for binding prediction in single letter amino acid code.
  • TepiTool (http://tools.iedb.org/tepitool/)
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Figures

Videos

Literature Cited

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Internet Resources
  http://tools.iedb.org/tepitool
  TepiTool: The newly developed online tool described in this protocol, for prediction of peptides binding to MHC class I and class II molecules.
  http://tools.iedb.org/
  IEDB's analysis resource: A collection of tools for the prediction and analysis of immune epitopes.
  http://www.imgt.org/
  International ImMunoGeneTics Information system (IMGT): An integrated knowledge resource for the immunoglobulins or antibodies, T cell receptors, and major histocompatibility of human and other vertebrate species.
  http://hla.alleles.org
  HLA nomenclature Web site: Web site describing HLA allele nomenclature.
  http://www.ebi.ac.uk/ipd/mhc/
  Immuno Polymorphism Database (IPD‐MHC): A centralized repository for sequences of the Major Histocompatibility Complex (MHC) from a number of different species and information on their nomenclature.
  http://www.allelefrequencies.net/
  Allelefrequencies.net database: Database with frequencies of HLA alleles.
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