tcren documentation

tcren is a Python re-implementation of the TCRen method for structure-based prediction of T-cell-receptor recognition of epitopes. It parses TCR–peptide–MHC structures, annotates TCR chains via arda, computes residue contacts, derives and applies residue-level statistical potentials, and scores candidate epitopes.

Contents

• Getting started
  • Installation
  • Command line
  • Library
  • Data
• Performance
  • Threading model
• API reference
  • tcren package

Tutorials

• 2D complementarity maps
• 3D peptide-binding pocket with CDR overlay
• The canonical TCR-pMHC frame — figures & summary
• PyMOL renders of canonically-oriented TCR-pMHC complexes
• Contact thresholds & bond types across all region pairs
• MHC pseudosequence (MPS) vs. peptide contacts
• Example — GILGFVFTL / HLA-A*02:01 and the CDR3β Arg–Ser motif
• TCRen potential & contact-statistics analysis

Indices

• Index

• Module Index