---
license: cc-by-4.0
tags:
- immunology
- tcr
- pmhc
- structural-biology
---

# isalgo/tcren_structures

TCR:peptide:MHC structure sets and benchmarks for **TCRen2** (structure-based prediction of TCR
recognition). Fetch with `tcren` / the manuscript `scripts/bootstrap_data.py`.

**Contents rule:** structures as `.gz`/`.tar.gz` (LFS) and `.txt`/`.md` descriptions only —
no notebooks, figures, or analysis tables.

## Layout

| folder | task | contents |
|---|---|---|
| `Native2026/`, `Canonical2026/` | derivation / ergodicity | non-redundant TCR:pMHC structures (`.gz`) |
| `Native2022/`, `PolyV2022/` | 2022-paper reproduction | structure sets (`.gz`) |
| `tcrvdb/` | TCR-ranking (specificity) | 618 TCRmodel2 models (`<hash>.pdb`) |
| `cpl/pdb_cpl/` | peptide-ranking (epitope) | peptide-swap best/worst, 5 TCRs |
| `as_case/` | MHC-ranking (B\*27:05 vs :02) | `as_case.tar.gz` + `content.md` |
| `Bobisse/`, `Bigot/` | neoantigen | cohort structures (`.gz`) |

## The three tasks

TCRen2 scores one interface-decomposed recognition energy Φ (TCRen for TCR:peptide, Miyazawa–Jernigan
for the presentation interfaces) and reads it three ways: rank **peptides** for a TCR:MHC (epitope /
neoantigen), rank **TCRs** for a pMHC (specificity), rank **MHC alleles** for a TCR:peptide (allele
restriction, e.g. ankylosing spondylitis B\*27:05 vs :02).