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isalgo/tcren_structures

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/… See the full description on the dataset page: https://huggingface.co/datasets/isalgo/tcren_structures.

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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`)
`vdjdb_binder_benchmark/`	TCR-ranking (real binders vs mock)	1,089 PDBs (`.tar.gz`) + `metadata.tsv` (labels, ipTM, tcren scores, covered/uncovered flag); see its `README.md`
`vdjdb_mut2023_benchmark/`	TCR-recognition control, one epitope	81 PDBs (`.tar.gz`) + `metadata.tsv`: HPVGEADYFEY crystals, their Rosetta mutants and TCRmodel2 mock decoys; see its `README.md`
`immrep23_negatives/`	TCR-ranking, extra decoys	832 of 2,985 modelled IMMREP mismatched pairings (run in progress); lifts the per-epitope decoy ceiling
`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).