Discovering TCR-Epitope-HLA Interactions

trimap-tools is a package for analysis of peptide-HLA presentation and TCR specificity. It is designed to help researchers understand the interactions between T cell receptors (TCRs) and peptides presented by human leukocyte antigen (HLA) molecules, which play a crucial role in the immune response.

🚀 Key Features of trimap-tools

• Peptide representation learning with HLA context
  Learns latent embeddings of peptides while incorporating HLA background, enabling biologically informed modeling.

• TCR specificity prediction using full receptor sequences
  Supports comprehensive modeling of TCR recognition by leveraging both α and β chain CDR regions.

• Visualization of critical TCR residues
  Highlights key amino acid positions in TCRs that contribute to antigen recognition, aiding biological interpretation.

• Discovery of disease-associated epitopes
  Identifies novel peptides potentially involved in disease by integrating small-scale disease-specific data with large-scale public datasets.

🔧 Components

• trimap.model.HLA_vae — Variational Autoencoder for HLA sequences

• trimap.model.PEP_vae — Variational Autoencoder for peptide sequences

• trimap.model.THE — Main prediction module integrating TCRs with peptide or HLA targets

📁 Sections

• Tutorials
  Step-by-step guides for training HLA/peptide encoders and predicting TCR specificity using example or custom data.

• Discover Disease-Associated Epitopes
  Learn how to integrate small-scale experimental data with large public datasets to uncover novel epitope–TCR interactions relevant to specific diseases.

Explore the sidebar to get started 👉
For installation instructions, pretrained models, or benchmarking datasets, refer to the corresponding sections.

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