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BMCBI
2006

Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores

9 years 2 months ago
Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores
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. Results: The kernel approach presented here shows increased prediction accuracy with a significantly higher number of true positives and negatives on multiple MHC class II alleles, when testing data sets from MHCPEP [1], MCHBN [2], and MHCBench [3]. Evaluation by cross validation, when seg...
Jesper Salomon, Darren R. Flower
Added 10 Dec 2010
Updated 10 Dec 2010
Type Journal
Year 2006
Where BMCBI
Authors Jesper Salomon, Darren R. Flower
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