MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit/implicit solvent models

• Published in: Briefings in bioinformatics 2021-11, Vol.22 (6)
• Main Authors: Ortiz-Mahecha, Carlos A, Agudelo, William A, Patarroyo, Manuel A, Patarroyo, Manuel E, Suárez, Carlos F
• Format: Article
• Language: English
• Subjects: Algorithms; Amino Acid Sequence; Computational Biology - methods; Histocompatibility Antigens - chemistry; Histocompatibility Antigens - immunology; Histocompatibility Antigens - metabolism; Humans; Ligands; Models, Molecular; Oligopeptides - chemistry; Oligopeptides - immunology; Oligopeptides - metabolism; Protein Binding; Quantum Theory; Software; Structure-Activity Relationship
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbab171

Experimentally estimating peptide-major histocompatibility complex (pMHC) binding affinity has been quite challenging due to the many receptors and the many potential ligands implicated in it. We have thus proposed a straightforward computational methodology considering the different mechanisms involved in pMHC binding to facilitate studying such receptor-ligand interactions. We have developed a pipeline using semi-empirical quantum mechanical methods for calculating pMHC class I and II molecules' binding energy (BE). This pipeline can systematize the methodology for calculating pMHC system BE, enabling the rational design of T-cell epitopes to be used as pharmaceuticals and vaccines.