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 publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages337-348
Number of pages12
Volume4774 LNBI
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)03029743
ISSN (Electronic)16113349

Other

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

Fingerprint

Peptide T
Epitopes
T-Lymphocyte Epitopes
T-cells
Peptides
Affine transformation
Binders
Prediction
Immune Response
Nonlinear Dynamics
Computational methods
Linear Models
Combinatorial Complexity
HIV
T-Lymphocytes
Molecules
Computational Methods
Prediction Model
Experimentation
Nonlinear Model

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

You, L., Zhang, P., Bodén, M., & Brusic, V. (2007). Understanding prediction systems for HLA-binding peptides and T-Cell epitope identification. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 4774 LNBI, pp. 337-348). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4774 LNBI).

Understanding prediction systems for HLA-binding peptides and T-Cell epitope identification. / You, Liwen; Zhang, Ping; Bodén, Mikael; Brusic, Vladimir.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4774 LNBI 2007. p. 337-348 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4774 LNBI).

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

You, L, Zhang, P, Bodén, M & Brusic, V 2007, Understanding prediction systems for HLA-binding peptides and T-Cell epitope identification. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 4774 LNBI, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4774 LNBI, pp. 337-348, 2nd IAPR International Workshop on Pattern Recognition in Bioinformatics, PRIB 2007, Singapore, Singapore, 10/1/07.
You L, Zhang P, Bodén M, Brusic V. Understanding prediction systems for HLA-binding peptides and T-Cell epitope identification. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4774 LNBI. 2007. p. 337-348. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
You, Liwen ; Zhang, Ping ; Bodén, Mikael ; Brusic, Vladimir. / Understanding prediction systems for HLA-binding peptides and T-Cell epitope identification. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4774 LNBI 2007. pp. 337-348 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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