ACE

ACE optimizes pooled ELISpot assay design and deconvolution using a fine-tuned ESM-2 sequence-aware peptide clustering to improve identification of antigen-specific immunogenic peptides.

Key Features:

• Sequence-Aware Pooling Strategy: Uses a fine-tuned ESM-2 model to cluster peptides by immunological similarity and inform peptide-pool assignments.
• Customizable Assay Design: Accepts user-defined parameters to generate optimized peptide-pool assignments tailored to experimental requirements.
• Efficient Deconvolution of Pool Spot Counts: Implements a deconvolution algorithm that processes ELISpot readouts to identify immunogenic peptides from positive pools.
• High-Throughput Capability: Supports scalable pooled ELISpot designs intended for large-scale studies and high-throughput screening.

Scientific Applications:

• Epitope immunogenicity validation: Validates predicted epitopes by identifying immunogenic peptides from pooled ELISpot data.
• Cancer immunology: Applies optimized pooled ELISpot designs to quantify antigen-specific T-cell reactivity in cancer research.
• Infectious disease immunology: Applies optimized pooled ELISpot designs to quantify antigen-specific T-cell reactivity in infectious disease research.
• High-throughput peptide screening: Enables large-scale identification of immunogenic peptides from complex peptide sets.

Methodology:

Peptides are clustered by a fine-tuned ESM-2 model to inform sequence-aware pooling, and a deconvolution algorithm processes ELISpot spot counts to pinpoint immunogenic peptides.