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A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes
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Docking-Based Prediction of Peptide Binding to MHC Proteins

Mariyana Atanasova1, Irini Doytchinova2

  • 1Faculty of Pharmacy, Medical University - Sofia, Sofia, Bulgaria. matanasova@pharmfac.mu-sofia.bg.

Methods in Molecular Biology (Clifton, N.J.)
|May 31, 2023
PubMed

Major histocompatibility complex (MHC) proteins are the most polymorphic and polygenic proteins in humans. They bind peptides, derived from cleavage of different pathogenic antigens, and are responsible for presenting them to T cells. The peptides recognized by the T cell receptors are denoted as epitopes and they trigger an immune response.In this chapter, we describe a docking protocol for predicting the peptide binding to a given MHC protein using the software tool GOLD. The protocol starts with the construction of a combinatorial peptide library used in the docking and ends with the derivation of a quantitative matrix (QM) accounting for the contribution of each amino acid at each peptide position.

Keywords:
Combinatorial libraryFlexible and rigid peptide dockingGOLDMolecular dockingPeptide-MHC binding predictionQuantitative matrix

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