SILVI

SILVI merges and filters HLA-binding prediction results to prioritize potentially immunogenic T-cell epitopes for peptide vaccine and immunotherapy design.

Key Features:

• Integration of HLA-binding predictions: Consolidates HLA-binding prediction outputs from multiple prediction servers and algorithms into a unified dataset.
• BLASTp host alignments: Performs BLASTp alignments against host proteins to identify mismatches and potential cross-reactivity.
• Physico-chemical property calculations: Computes physical-chemical properties of peptides, including hydrophobicity.
• Filtering by immunological metrics: Applies filters based on predicted IC50 values, hydrophobicity, and mismatches with host proteins to identify conserved, promiscuous, and strong-binding epitopes.
• Customizable filtering criteria: Provides script-based customization of filtering parameters and thresholds within an R implementation.
• Demonstrated datasets: Integrates prediction results and validated epitopes from example proteins derived from viral, bacterial, and parasitic microorganisms, including entries from the Immune Epitope Database (IEDB) and the Human Papillomavirus (HPV) proteome.

Scientific Applications:

• Peptide vaccine and immunotherapy design: Prioritizes candidate T-cell epitopes for inclusion in peptide-based vaccines and immunotherapies.
• Comparative immunoinformatics: Facilitates comparison and integration of results from multiple HLA-binding prediction algorithms to refine epitope selection.
• Cross-reactivity assessment: Reduces potential host cross-reactivity by incorporating BLASTp alignments against host proteins into selection criteria.

Methodology:

Merges HLA-binding prediction data with BLASTp alignments to host proteins and computed physico-chemical properties (including hydrophobicity), then applies default and user-defined filters based on predicted IC50, hydrophobicity, and host-protein mismatches to prioritize epitopes; implemented in R and demonstrated on viral, bacterial, and parasitic protein datasets including IEDB and HPV proteome entries.