Quantitative prediction of MHC-II peptide binding affinity using relevance vector machine |
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Authors: | Wen Zhang Juan Liu Yanqing Niu |
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Affiliation: | (1) Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA |
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Abstract: | Peptide-MHC binding is an important prerequisite event and has immediate consequences to immune response. Those peptides binding
to MHC molecules can activate the T-cell immunity, and they are useful for understanding the immune mechanism and developing
vaccines for diseases. Accurate prediction of the binding between peptides and MHC-II molecules has long been a challenge
in bioinformatics. Recently, instead of differentiating peptides as binder or non-binder, researchers are more interested
in making predictions directly on peptide binding affinities. In this paper, we investigate the use of relevance vector machine
to quantitatively predict the binding affinities between MHC-II molecules and peptides. In our scheme, a new encoding scheme
is used to generate the input vectors, and then by using relevance vector machine we develop the prediction models on the
basis of binding cores, which are recognized in an iterative self-consistent way. When applied to three MHC-II molecules DRB1*0101,
DRB1*0401 and DRB1*1501, our method produces consistently better performance than several popular quantitative methods, in
terms of cross-validated squared error, cross-validated correlation coefficient, and area under ROC curve. All evidences indicate
that our method is an effective tool for MHC-II binding affinity prediction. |
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Keywords: | |
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