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Semi-empirical quantum evaluation of peptide – MHC class II binding

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Autores
González, Ronald
Suárez C.F.
Bohórquez H.J.
Patarroyo M.A.
Patarroyo M.E.

Fecha
2017

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Elsevier B.V.

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Abstract
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.
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Keywords
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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