Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores |
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Authors: | Jesper Salomon and Darren R Flower |
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Institution: | (1) The Jenner Institute, University of Oxford, Compton, Newbury, Berkshire, RG20 7NN, UK |
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Abstract: | Background Modelling the interaction between potentially antigenic peptides and Major Histocompatibility Complex (MHC) molecules is a
key step in identifying potential T-cell epitopes. For Class II MHC alleles, the binding groove is open at both ends, causing
ambiguity in the positional alignment between the groove and peptide, as well as creating uncertainty as to what parts of
the peptide interact with the MHC. Moreover, the antigenic peptides have variable lengths, making naive modelling methods
difficult to apply. This paper introduces a kernel method that can handle variable length peptides effectively by quantifying
similarities between peptide sequences and integrating these into the kernel. |
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Keywords: | |
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