Static energy analysis of MHC class I and class II peptide-binding affinity

Matthew N. Davies, Darren R. Flower

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Abstract

Antigenic peptide is presented to a T-cell receptor (TCR) through the formation of a stable complex with a major histocompatibility complex (MHC) molecule. Various predictive algorithms have been developed to estimate a peptide's capacity to form a stable complex with a given MHC class II allele, a technique integral to the strategy of vaccine design. These have previously incorporated such computational techniques as quantitative matrices and neural networks. A novel predictive technique is described, which uses molecular modeling of predetermined crystal structures to estimate the stability of an MHC class II-peptide complex. The structures are remodeled, energy minimized, and annealed before the energetic interaction is calculated.
Original languageEnglish
Title of host publicationImmunoinformatics
Subtitle of host publicationpredicting immunogenicity in silico
EditorsDarren R. Flowers
Place of PublicationTotowa, NJ (US)
PublisherHumana Press
Pages309-320
Number of pages12
ISBN (Electronic)978-1-60327-118-9
ISBN (Print)978-1-58829-699-3
DOIs
Publication statusPublished - 16 Jul 2007

Publication series

NameMethods in molecular biology™
PublisherHumana Press
Volume409
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Fingerprint

Major Histocompatibility Complex
Peptides
T-Cell Antigen Receptor
Vaccines
Alleles

Keywords

  • computational biology
  • computer simulation
  • protein databases
  • histocompatibility antigens class I
  • histocompatibility antigens class II
  • humans
  • immunogenetics
  • major histocompatibility complex
  • peptides
  • protein binding
  • quantitative structure-activity relationship
  • software
  • thermodynamics
  • simulated annealing
  • energy minimization
  • antigenic peptides
  • MHC

Cite this

Davies, M. N., & Flower, D. R. (2007). Static energy analysis of MHC class I and class II peptide-binding affinity. In D. R. Flowers (Ed.), Immunoinformatics: predicting immunogenicity in silico (pp. 309-320). (Methods in molecular biology™; Vol. 409). Totowa, NJ (US): Humana Press. https://doi.org/10.1007/978-1-60327-118-9_23
Davies, Matthew N. ; Flower, Darren R. / Static energy analysis of MHC class I and class II peptide-binding affinity. Immunoinformatics: predicting immunogenicity in silico. editor / Darren R. Flowers. Totowa, NJ (US) : Humana Press, 2007. pp. 309-320 (Methods in molecular biology™).
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Davies, MN & Flower, DR 2007, Static energy analysis of MHC class I and class II peptide-binding affinity. in DR Flowers (ed.), Immunoinformatics: predicting immunogenicity in silico. Methods in molecular biology™, vol. 409, Humana Press, Totowa, NJ (US), pp. 309-320. https://doi.org/10.1007/978-1-60327-118-9_23

Static energy analysis of MHC class I and class II peptide-binding affinity. / Davies, Matthew N.; Flower, Darren R.

Immunoinformatics: predicting immunogenicity in silico. ed. / Darren R. Flowers. Totowa, NJ (US) : Humana Press, 2007. p. 309-320 (Methods in molecular biology™; Vol. 409).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

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AB - Antigenic peptide is presented to a T-cell receptor (TCR) through the formation of a stable complex with a major histocompatibility complex (MHC) molecule. Various predictive algorithms have been developed to estimate a peptide's capacity to form a stable complex with a given MHC class II allele, a technique integral to the strategy of vaccine design. These have previously incorporated such computational techniques as quantitative matrices and neural networks. A novel predictive technique is described, which uses molecular modeling of predetermined crystal structures to estimate the stability of an MHC class II-peptide complex. The structures are remodeled, energy minimized, and annealed before the energetic interaction is calculated.

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KW - quantitative structure-activity relationship

KW - software

KW - thermodynamics

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KW - energy minimization

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Davies MN, Flower DR. Static energy analysis of MHC class I and class II peptide-binding affinity. In Flowers DR, editor, Immunoinformatics: predicting immunogenicity in silico. Totowa, NJ (US): Humana Press. 2007. p. 309-320. (Methods in molecular biology™). https://doi.org/10.1007/978-1-60327-118-9_23