PAComplex

PAComplex analyzes pMHC and peptide-TCR interactions to identify significantly similar TCR-pMHC templates, infer homologous peptide antigens from pathogen genome databases, and produce detailed interaction models.

Key Features:

• Dual Interface Analysis: Investigates both pMHC and peptide-TCR interactions within the same analysis framework.
• Template Identification: Identifies significantly similar TCR-pMHC templates using antibody-antigen and protein-protein interaction scoring matrices.
• Homologous Peptide Antigen Inference: Searches extensive pathogen genome databases for homologous peptide antigens related to the query.
• Detailed Interaction Models: Outputs interaction models with visualizations of hydrogen bonds and steric interactions at both pMHC and peptide-TCR interfaces.
• High Prediction Accuracy: Reports high prediction accuracy in identifying potential peptide antigens across various pathogens.

Scientific Applications:

• Peptide Vaccine Design: Identifies candidate peptide antigens for vaccine development targeting specific pathogens.
• Understanding MHC Restriction: Provides insights into peptide presentation by MHC molecules and recognition by TCRs to inform immunotherapy design.

Methodology:

Uses specialized scoring matrices for peptide-TCR and pMHC interactions, employs antibody-antigen and protein-protein interaction scoring for template identification, performs extensive searches of pathogen genome databases for homologous peptides, and generates detailed model visualizations of hydrogen bonds and steric interactions.