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

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 invo...

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Bibliographic Details
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
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Summary: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.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbab171