Abstract
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.
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Acknowledgment
This work was supported by the Science and Education for Smart Growth Operational Program and co-financed by the European Union through the European Structural and Investment funds (Grant No BG05M2OP001-1.001-0003).
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Atanasova, M., Doytchinova, I. (2023). Docking-Based Prediction of Peptide Binding to MHC Proteins. In: Reche, P.A. (eds) Computational Vaccine Design. Methods in Molecular Biology, vol 2673. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3239-0_17
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DOI: https://doi.org/10.1007/978-1-0716-3239-0_17
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