Understanding prediction systems for HLA-binding peptides and T-Cell epitope identification

Liwen You, Ping Zhang, Mikael Bodén, Vladimir Brusic

Research output: Chapter in Book/Report/Conference proceedingConference contribution

8 Citations (Scopus)

Abstract

Peptide binding to HLA molecules is a critical step in induction and regulation of T-cell mediated immune responses. Because of combinatorial complexity of immune responses, systematic studies require combination of computational methods and experimentation. Most of available computational predictions are based on discriminating binders from non-binders based on use of suitable prediction thresholds. We compared four state-of-the-art binding affinity prediction models and found that nonlinear models show better performance than linear models. A comprehensive analysis of HLA binders (A*0101, A*0201, A*0301, A*1101, A*2402, B*0702, B*0801 and B*1501) showed that non-linear predictors predict peptide binding affinity with high accuracy. The analysis of known T-cell epitopes of survivin and known HIV T-cell epitopes showed lack of correlation between binding affinity and immunogenicity of HLA-presented peptides. T-cell epitopes, therefore, can not be directly determined from binding affinities by simple selection of the highest affinity binders.

Original languageEnglish
Title of host publicationPattern Recognition in Bioinformatics - Second IAPR International Workshop, PRIB 2007, Proceedings
PublisherSpringer Verlag
Pages337-348
Number of pages12
ISBN (Print)9783540752851
DOIs
Publication statusPublished - 2007
Externally publishedYes
Event2nd IAPR International Workshop on Pattern Recognition in Bioinformatics, PRIB 2007 - Singapore, Singapore
Duration: Oct 1 2007Oct 2 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4774 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other2nd IAPR International Workshop on Pattern Recognition in Bioinformatics, PRIB 2007
CountrySingapore
CitySingapore
Period10/1/0710/2/07

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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