| # CPL — combinatorial peptide library structures (cpl_structures.tar.gz) |
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| 7 TCR clones (1e6, 4c6, 868, ila1, mel5, mel8, sb27), best- vs worst-peptide AlphaFold C-beta peptide-swap models — 2103 PDB files (per-clone best/worst dirs inside the archive). |
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| All seven clones now carry a model of their OWN cognate epitope in the best half: |
| 1e6/ALWGPDPAAA, 4c6/LWMRLLPLL, 868/SLYNTVATL, ila1/ILAKFLHWL, mel5/ELAGIGILTV, mel8/EAAGIGILTV, |
| sb27/LPEPLPQGQLTAY. The sb27 one (added 2026-07-27) was modelled after the other 2102 on the same |
| receptor and MHC coordinates — chains A/B/D are byte-for-byte the other sb27 models', only the |
| 13-mer peptide differs — but it is NOT part of the original library deposit, so anything that |
| counts "structures per clone" should mark it separately. |
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| 868's cognate is SLYNTVATL (HIV-1 Gag p17 SL9), NOT SIFLFIARV. SIFLFIARV is one of its own library |
| peptides and was recorded as the cognate until 2026-07-27; because the clone → crystal lookup was |
| keyed on that string it matched nothing, and the pipeline reported that 868 had no deposited |
| crystal. It has four: 5NME (the index complex, SLYNTVATL), 5NMD (unligated receptor), 5NMF (6I) and |
| 5NMG (3F6I8V). |
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| # cpl_native_structures.tar.gz — the deposited complexes |
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| 27 RCSB entries covering all seven clones. The cognate complex per clone is |
| 1e6→3UTS, 4c6→7NMG, 868→5NME, ila1→5MEN, mel5→3HG1, mel8→7Q9B, sb27→2AK4; the rest are the same |
| receptors on variant peptides. MATCH ON THE RECEPTOR (CDR3α/CDR3β pair), never on the epitope: a |
| peptide identifies neither side uniquely, and EAAGIGILTV in particular occurs both in MEL8's own |
| 7Q9B and in 4QOK, whose receptor is MEL5. 7Q9B is held here as PDB (transferred from Native2026); |
| it was previously mmCIF-only, which made it invisible to a `*.pdb` glob. |
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| Peptide-ranking benchmark: AUC of -TCRen(TCR:peptide), best(+) vs worst(-), per clone and pooled. |
| Provenance: structures COMPUTED (AF peptide-swap); best/worst labels from EXPERIMENTAL combinatorial peptide-library positional scans (Sewell/Cole lab; see DATASETS.md per-clone references). |
| Source: aldan3 /projects/structures/CPL_data_to_hf/pdb_cpl/. |
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