Methods for prediction of peptide binding to MHC molecules: a comparative study

Kun Yu, Christian Schonbach, Nikolai Petrovsky, Judice Koh, Vladimir Brusic

Research output: Contribution to journalArticle

114 Citations (Scopus)

Abstract

BACKGROUND: A variety of methods for prediction of peptide binding to major histocompatibility complex (MHC) have been proposed. These methods are based on binding motifs, binding matrices, hidden Markov models (HMM), or artificial neural networks (ANN). There has been little prior work on the comparative analysis of these methods. MATERIALS AND METHODS: We performed a comparison of the performance of six methods applied to the prediction of two human MHC class I molecules, including binding matrices and motifs, ANNs, and HMMs. RESULTS: The selection of the optimal prediction method depends on the amount of available data (the number of peptides of known binding affinity to the MHC molecule of interest), the biases in the data set and the intended purpose of the prediction (screening of a single protein versus mass screening). When little or no peptide data are available, binding motifs are the most useful alternative to random guessing or use of a complete overlapping set of peptides for selection of candidate binders. As the number of known peptide binders increases, binding matrices and HMM become more useful predictors. ANN and HMM are the predictive methods of choice for MHC alleles with more than 100 known binding peptides. CONCLUSION: The ability of bioinformatic methods to reliably predict MHC binding peptides, and thereby potential T-cell epitopes, has major implications for clinical immunology, particularly in the area of vaccine design.
Original languageEnglish
Pages (from-to)137-148
Number of pages12
JournalMolecular Medicine
Volume8
Issue number3
Publication statusPublished - 2002
Externally publishedYes

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Major Histocompatibility Complex
Peptides
Mass Screening
T-Lymphocyte Epitopes
Allergy and Immunology
Computational Biology
Vaccines
Alleles
Proteins

Cite this

Yu, K., Schonbach, C., Petrovsky, N., Koh, J., & Brusic, V. (2002). Methods for prediction of peptide binding to MHC molecules: a comparative study. Molecular Medicine, 8(3), 137-148.
Yu, Kun ; Schonbach, Christian ; Petrovsky, Nikolai ; Koh, Judice ; Brusic, Vladimir. / Methods for prediction of peptide binding to MHC molecules: a comparative study. In: Molecular Medicine. 2002 ; Vol. 8, No. 3. pp. 137-148.
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Yu, K, Schonbach, C, Petrovsky, N, Koh, J & Brusic, V 2002, 'Methods for prediction of peptide binding to MHC molecules: a comparative study', Molecular Medicine, vol. 8, no. 3, pp. 137-148.

Methods for prediction of peptide binding to MHC molecules: a comparative study. / Yu, Kun; Schonbach, Christian; Petrovsky, Nikolai; Koh, Judice; Brusic, Vladimir.

In: Molecular Medicine, Vol. 8, No. 3, 2002, p. 137-148.

Research output: Contribution to journalArticle

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AU - Yu, Kun

AU - Schonbach, Christian

AU - Petrovsky, Nikolai

AU - Koh, Judice

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AB - BACKGROUND: A variety of methods for prediction of peptide binding to major histocompatibility complex (MHC) have been proposed. These methods are based on binding motifs, binding matrices, hidden Markov models (HMM), or artificial neural networks (ANN). There has been little prior work on the comparative analysis of these methods. MATERIALS AND METHODS: We performed a comparison of the performance of six methods applied to the prediction of two human MHC class I molecules, including binding matrices and motifs, ANNs, and HMMs. RESULTS: The selection of the optimal prediction method depends on the amount of available data (the number of peptides of known binding affinity to the MHC molecule of interest), the biases in the data set and the intended purpose of the prediction (screening of a single protein versus mass screening). When little or no peptide data are available, binding motifs are the most useful alternative to random guessing or use of a complete overlapping set of peptides for selection of candidate binders. As the number of known peptide binders increases, binding matrices and HMM become more useful predictors. ANN and HMM are the predictive methods of choice for MHC alleles with more than 100 known binding peptides. CONCLUSION: The ability of bioinformatic methods to reliably predict MHC binding peptides, and thereby potential T-cell epitopes, has major implications for clinical immunology, particularly in the area of vaccine design.

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Yu K, Schonbach C, Petrovsky N, Koh J, Brusic V. Methods for prediction of peptide binding to MHC molecules: a comparative study. Molecular Medicine. 2002;8(3):137-148.