RosettaMHC

RosettaMHC models peptide–MHC complexes to enable structure-based characterization of SARS-CoV-2 peptides presented by the HLA-A*02:01 allele for CD8+ T cell epitope analysis.

Key Features:

• Comparative modeling strategy: Employs a comparative modeling approach using experimentally determined peptide/MHC structures to build models of peptide/HLA complexes.
• Use of PDB X-ray structures: Utilizes high-resolution X-ray peptide/MHC structures from the Protein Data Bank (PDB) as templates for modeling.
• Three-dimensional model generation: Produces physically realistic three-dimensional models of SARS-CoV-2 epitopes bound to HLA-A*02:01.
• Allele and epitope coverage: Focuses on the HLA-A*02:01 allele and models 439 predicted 9mer and 279 predicted 10mer SARS-CoV-2 epitopes.

Scientific Applications:

• CD8+ T cell epitope characterization: Enables structural analysis of peptides that may be presented to CD8+ T cells in the context of HLA-A*02:01.
• Structure–immunogenicity correlation: Supports exploration of how structural features of peptide/HLA complexes relate to immunogenic properties.
• Cross-study structural comparison: Provides modeled peptide/HLA structures that can be used to compare antigen presentation across studies and strains.

Methodology:

Performs comparative modeling using high-resolution X-ray peptide/MHC structures from the Protein Data Bank (PDB) to generate three-dimensional models of SARS-CoV-2 9mer and 10mer epitopes bound to HLA-A*02:01.