HLArestrictor

HLArestrictor predicts patient-specific HLA restriction elements and minimal optimal epitopes within peptides to facilitate T cell epitope identification.

Key Features:

• Integration with NetMHCpan: Leverages the NetMHCpan predictor to identify MHC restriction elements and corresponding minimal epitopes optimized for individual HLA profiles.
• High-resolution input requirement: Requires high-resolution (4-digit) HLA typing to generate precise, patient-specific predictions.
• Peptide binding prediction: Predicts all potential 8–11mer peptide binders within larger peptides and reports predicted HLA restrictions and minimal epitopes.
• Validation and performance: Validated on an HIV IFNγ ELIspot peptide response dataset, identifying HLA restrictions and minimal epitopes for approximately 90% of positive peptide/patient pairs and rejecting over 95% of negative peptide–HLA pairs.
• Tetramer validation: Accurately predicted both HLA restriction elements and minimal epitopes for all 18 peptide/HLA responses validated by tetramer assays.

Scientific Applications:

• T cell epitope discovery: Identifying patient-specific T cell epitopes from peptide screening data.
• Infectious disease and disease-model mapping: Mapping epitopes in infectious diseases (including HIV) and other disease models where individual HLA-specific responses are relevant.
• Experimental prioritization and immunotherapy development: Prioritizing candidate epitopes for experimental validation and for development of personalized immunotherapies.

Methodology:

Uses NetMHCpan peptide-binding predictions with high-resolution (4-digit) HLA typing to evaluate all 8–11mer peptides within larger sequences and assign HLA restriction elements and minimal epitopes.