| 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). | |