© 2016 Elsevier B.V.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.
González, R., Suárez, C. F., Bohórquez, H. J., Patarroyo, M. A., & Patarroyo, M. E. (2017). Semi-empirical quantum evaluation of peptide – MHC class II binding. Chemical Physics Letters, 29-34. https://doi.org/10.1016/j.cplett.2016.12.015