Alithea Bio Launches HLA-Compass Binding Prediction

Faster, more confident peptide–MHC decisions—now built directly into HLA-Compass

Alithea Bio is excited to announce the launch of its HLA-Compass Binding Prediction AI,
a powerful new capability designed to accelerate and de-risk peptide–MHC decision-making in
immunotherapy, vaccine development, and immunopeptidomics research.

This is more than just another binding predictor. Trained on the largest human immunopeptidomics dataset
and seamlessly integrated into HLA-Compass, it is built for scientists who need precision, scale,
and confidence—from early discovery through translational research.

Why Peptide–MHC Binding Prediction Matters

Identifying which peptides bind to specific HLA alleles is a foundational challenge in:

• Cancer immunotherapy and neoantigen discovery
• Therapeutic and prophylactic vaccine development
• Off-target risk assessment
• Immunopeptidomics and antigen presentation studies

Many existing prediction tools rely heavily on in vitro binding affinity assays, offer limited coverage
of human HLA diversity, or operate in fragmented workflows that slow down discovery.

HLA-Compass Binding Prediction AI was built to change that.

Binding Prediction—Now Inside HLA-Compass

Starting today, users can predict peptide–MHC binding directly within HLA-Compass, eliminating the need
for external tools or manual data transfers.

Researchers can:

• Input peptide lists or full protein FASTA sequences
• Specify HLA class I alleles of interest
• Run predictions in seconds
• Export predicted binders as TSV or CSV files for downstream analysis, triage, and reporting

All within a single, unified platform.

Two Flexible Analysis Modes

Simple Mode — Rapid, On-Demand Predictions

Designed for speed and ease of use, Simple Mode allows researchers to:

• Paste short peptide lists (8–15 amino acids) or upload them as a file
• Upload protein FASTA sequences
• Quickly evaluate binding across selected HLA alleles

Ideal for fast, precise predictions on datasets of up to 25,000 peptides.

Multi-Sample Mode — Scalable Analysis from DDA Output

For larger and more complex studies, Multi-Sample Mode supports:

• DDA-derived immunopeptidomics datasets with associated metadata
• Predictions across multiple samples and HLA backgrounds

This mode is well suited for immunopeptidomics workflows and clinical applications.

What Makes Alithea’s Predictor Different

🎯 Higher Precision Where It Counts

Alithea’s Binding Prediction AI delivers high precision and recall across HLA alleles, helping scientists
focus on the most biologically relevant candidates while reducing false positives.

🧪 Trained on Mass-Spectrometry–Verified Ligands

Unlike many predictors trained primarily on binding assays, this model is trained on
mass-spectrometry–verified HLA ligands—real peptides presented on real human cells.

That means predictions are grounded in true antigen presentation biology, not just theoretical binding affinity.

🌍 Rare-Allele Coverage for Global Applicability

The model includes expanded coverage of rare and underrepresented HLA alleles, enabling more inclusive
research across diverse populations—critical for global vaccine and immunotherapy development.

Built for Immunopeptidomics, Immunotherapy, and Drug Discovery

HLA-Compass Binding Prediction AI is purpose-built for teams working in:

• Oncology and cancer vaccines
• T-cell–based immunotherapies
• Drug discovery and target validation
• Off-target risk and safety assessment
• Proteomics and immunopeptidomics workflows

By combining experimental evidence, AI-driven prediction, and integrated workflows, Alithea Bio helps
researchers move faster—without compromising confidence.

From Prediction to Decision—Faster Than Ever

With binding prediction now embedded in HLA-Compass, researchers can:

• Reduce tool fragmentation through integrated, end-to-end analysis
• Shorten analysis cycles from data to insight
• Make earlier, more confident go/no-go decisions

All while working within a platform designed around real-world immunopeptidomics data.

Start Using HLA-Compass Binding Prediction AI Today

The HLA-Compass Binding Prediction AI is live and available now.

Whether you’re evaluating a handful of peptides or analyzing cohort-scale datasets, Alithea Bio is
redefining how peptide–MHC binding decisions are made—faster, smarter, and with human evidence at the core.

Interested in seeing it in action? Explore HLA-Compass or contact the Alithea Bio team to learn how
Binding Prediction AI can accelerate your research.