Semi-empirical quantum evaluation of peptide – MHC class II binding
Peptide presentation by the major histocompatibility complex (MHC) is a key process for triggering a specific immune response. Studying peptide-MHC (pMHC) binding from a structural-based approach has potential for reducing the costs of investigation into vaccine development. This study involved using two semi-empirical quantum chemistry methods (PM7 and FMO-DFTB) for computing the binding energies of peptides bonded to HLA-DR1 and HLA-DR2. We found that key stabilising water molecules involved in the peptide binding mechanism were required for finding high correlation with IC50 experimental values. Our proposal is computationally non-intensive, and is a reliable alternative for studying pMHC binding interactions. © 2016 Elsevier B.V.
Bins ; Molecules ; Peptides ; Quantum chemistry ; Binding interaction ; Experimental values ; FMO-DFTB ; HLA-DR ; Major histocompatibility complex ; Quantum chemistry methods ; Receptor-ligand interactions ; Vaccine development ; Binding energy ; FMO-DFTB ; HLA-DR ; PM7 ; Receptor-ligand interactions ;
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