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Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes

Authors:

Sinu Paul,

John Sidney,

Bjoern Peters,

Alessandro SetteAuthors Info & Claims

BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

Pages 733 - 738

https://doi.org/10.1145/2649387.2660842

Published: 20 September 2014 Publication History

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Abstract

Computational prediction of HLA class II restricted T cell epitopes has great significance in many immunological studies including vaccine discovery. With the development of novel bioinformatics approaches, prediction of HLA class II binding has improved significantly but a strategy to predict the most dominant HLA class II epitopes has not been defined. Using different sets of peptides from various allergen and bacterial antigens and HLA class II binding prediction tools from the IEDB, we have designed a strategy to predict the top epitopes from any antigen. We found that the top 21% of 15-mer peptides overlapping by 10 residues (based on the predicted binding to seven DRB1 and DRB3/4/5 alleles) capture 50% of the immune response. This corresponded to an IEDB consensus percentile rank of 19.82 which could be used as a universal prediction threshold.

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Cited By

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Hossen MHasan MHaque MAl Arian THalder SUddin MAbdullah-Al-Mamun MShakil M(2023)Immunoinformatics-aided rational design of multiepitope-based peptide vaccine (MEBV) targeting human parainfluenza virus 3 (HPIV-3) stable proteinsJournal of Genetic Engineering and Biotechnology10.1186/s43141-023-00623-521:1(162)Online publication date: Dec-2023
https://doi.org/10.1186/s43141-023-00623-5
Bresciani APaul SSchommer NDillon MBancroft TGreenbaum JSette ANielsen MPeters B(2016)T‐cell recognition is shaped by epitope sequence conservation in the host proteome and microbiomeImmunology10.1111/imm.12585148:1(34-39)Online publication date: 8-Feb-2016
https://doi.org/10.1111/imm.12585
Ponomarenko JVaughan KPaul SPeters BSette AHaeussler MMaurer-Stroh S(2015)Ebola: an analysis of immunity at the molecular level2015 International Workshop on Artificial Immune Systems (AIS)10.1109/AISW.2015.7469230(1-8)Online publication date: Jul-2015
https://doi.org/10.1109/AISW.2015.7469230

Index Terms

Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes
1. Applied computing
  1. Life and medical sciences

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Published In

BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

September 2014

851 pages

ISBN:9781450328944

DOI:10.1145/2649387

General Chairs:
Pierre Baldi
University of California, Irvine
,
Wei Wang
University of California, Los Angeles

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 20 September 2014

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National Institute of Allergy and Infectious Diseases

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BCB '14

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SIGBio

BCB '14: ACM-BCB '14

September 20 - 23, 2014

California, Newport Beach

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Overall Acceptance Rate 254 of 885 submissions, 29%

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Cited By

View all

Hossen MHasan MHaque MAl Arian THalder SUddin MAbdullah-Al-Mamun MShakil M(2023)Immunoinformatics-aided rational design of multiepitope-based peptide vaccine (MEBV) targeting human parainfluenza virus 3 (HPIV-3) stable proteinsJournal of Genetic Engineering and Biotechnology10.1186/s43141-023-00623-521:1(162)Online publication date: Dec-2023
https://doi.org/10.1186/s43141-023-00623-5
Bresciani APaul SSchommer NDillon MBancroft TGreenbaum JSette ANielsen MPeters B(2016)T‐cell recognition is shaped by epitope sequence conservation in the host proteome and microbiomeImmunology10.1111/imm.12585148:1(34-39)Online publication date: 8-Feb-2016
https://doi.org/10.1111/imm.12585
Ponomarenko JVaughan KPaul SPeters BSette AHaeussler MMaurer-Stroh S(2015)Ebola: an analysis of immunity at the molecular level2015 International Workshop on Artificial Immune Systems (AIS)10.1109/AISW.2015.7469230(1-8)Online publication date: Jul-2015
https://doi.org/10.1109/AISW.2015.7469230

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Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens

Beyond B-Cell Epitopes: Curating Positive Data on Antipeptide Paratope Binding to Support Development of Computational Tools for Vaccine Design and Other Translational Applications

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