Masters Degrees (Applied Mathematics)

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Browsing Masters Degrees (Applied Mathematics) by Author "Daumas, Tshenolo Thato Eustacia"

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    The Impact of peptide flanking residues on predicting peptide-MHC-II binding interactions using convolutional Neural Networks
    (Stellenbosch : Stellenbosch University, 2022-04) Daumas, Tshenolo Thato Eustacia; Bah, Bubacarr; Degoot, Abdoelnaser M.; Ndifon, Wilfred; Stellenbosch University. Faculty of Science. Dept. of Mathematical Sciences (Applied Mathematics)
    ENGLISH ABSTRACT: Major histocompatibility complex class II (MHC-II) is one of three classes of MHC molecules and is located on the surface of professional antigen presenting cells. MHC-II molecules present antigenic peptides derived from pathogens that cause infection, for recognition by CD4+ T lymphocytes. MHC-II molecules are critical components of the chain of intercellular interactions required for the adaptive im- mune response to be launched successfully, as this chain is thought to begin with the binding of antigenic peptides by MHC-II molecules. While considerable progress in computational efforts have been made towards un- derstanding peptide-MHC interactions for classes I and II, the case for peptide- MHC-II remains challenging due to MHC-II molecules being highly polymorphic and having open-ended binding grooves. Consequently, MHC-II molecules interact with peptides of varying lengths; therefore, the role that peptide flanking residues (PFRs) play in peptide-MHC-II binding interactions must be considered. We pro- pose an allele-specific convolutional neural network model that simulates binding interactions between peptides and MHC-II molecules that also incorporates PFR information in the input. Deep learning models for peptide-MHC-II interactions that have been published, such as the allele-specific model, NetMHCII and the transallelic model NetMHCI- Ipan have demonstrated encouraging predictive performance. When compared, our proposed CNN model outperformed the latest version of the model, NetMHCII-2.3 across all MHC-II alleles considered with mean AUC value of 0.951 as compared with 0.822 for NetMHCII-3.2. Furthermore, we analysed the impact that PFRs have on modelling peptide-MHC-II binding interactions and laid the foundations of de- veloping a transallelic model based on the CNN model.