isalgo/vdjdb_structure_models

VDJdb structures, contacts and coordinate links

Native and predicted TCR:pMHC coordinates linked to VDJdb observations, with residue coordinates, contact tables and complementarity maps. Start from a current record ID and the reviewed link tables to select files for your receptor and peptide-MHC context.

Task	Start here
Find coordinates for a VDJdb record	Current record links
Find additional native, predicted or mutant coordinates	Supplemental catalogue
Retrieve complete deposited mmCIF sources	PDB sources and native review
Inspect historical withdrawn assignments	Separate collection and dispositions
Query receptors, retrieve motifs or inspect record confidence	VDJdb documentation

Download only what you need

Select a dataset commit from the revision history and set HF_REV to its full hash. Use that revision for metadata and coordinates. With uv installed, fetch the compact association tables first:

: "${HF_REV:?Set HF_REV to a dataset commit hash}"
uvx --from huggingface-hub hf download isalgo/vdjdb_structure_models \
  --repo-type dataset --revision "$HF_REV" --local-dir structures \
  metadata/current/record_links.tsv.gz metadata/current/asset_sources.tsv.gz \
  metadata/current/asset_inventory.tsv.gz metadata/current/verification.json

1. Select your record_id in record_links.tsv.gz. Compare the database snapshot and input identities in verification.json with your own database files.
2. Require matches_repaired for the built junction pair, or matches_original for the submitted pair. Require exact_tcr_pmhc_match for agreement on the pair, peptide, recorded species, both MHC chains and MHC class.
3. Join record_links.source_row to asset_sources.source_row, then join asset_sources.asset_row to asset_inventory.asset_row.
4. Select the desired archive type and deduplicate archive/member. Several source rows can link to the same file. Link counts are not counts of structures or experiments.

Set archive and member to the exact values from a selected inventory row:

: "${archive:?Set archive from the selected inventory row}"
: "${member:?Set member from the selected inventory row}"
uvx --from huggingface-hub hf download isalgo/vdjdb_structure_models \
  "data/$archive" --repo-type dataset --revision "$HF_REV" --local-dir structures
(set -C; tar -xOzf "structures/data/$archive" -- "$member" > selected-asset)

Check archive size and free disk before downloading. Selecting a tar member still requires downloading and scanning its archive; this command avoids extracting every file and refuses to overwrite an existing destination. Give the selected asset its appropriate .pdb, table or .svg extension afterwards.

For supplemental files, join that catalogue's record_links.tsv.gz to structures.tsv.gz by structure_id, retain sequence_state, and use its declared archive and member paths. This is a separate schema from the historical inventory. Its structure ID is the SHA256 of the exported uncompressed coordinate content.

Files and their units

Location	Contents
data/pdb_files.tgz	Predicted TCR:pMHC PDBs in a canonical coordinate frame
data/pdb_files_native.tgz	Experimental PDB structures processed into that frame
data/coordinates_aa.tgz	Per-residue C-alpha coordinate tables
data/contacts_aa.tgz	Residue pairs within 5 Å for TCR alpha/beta CDR3 and peptide
data/complementarity_maps.tgz, data/complementarity_maps_simplified.tgz	SVG projections of TCR CDR3 and peptide coordinates
vdjdb_structures_metadata.tsv.gz	Preserved historical source metadata and supplied model metrics
metadata/current/	Current-record associations, asset inventory, dispositions and verification
metadata/native_review/	Reviewed native dispositions and deposited-accession coverage
data/pdb_sources/	Complete deposited mmCIF sources, compressed, with a source manifest
metadata/supplemental/, data/supplemental/	Additional coordinate contents, metadata, record links and archives
low_confidence/withdrawn_10x/	A standalone partition of withdrawn assignments, retaining selected historical files
legacy_assets/	Historical supporting assets
tools/	Regeneration and verification programs; inspect each program's --help

The historical collection has 11,253 PDB files: 10,884 predicted and 369 native. Its reviewed accounting links 8,429 files to current record IDs, retains 2,811 files for withdrawn assignments, and preserves 13 excluded modified-ligand complexes. The current metadata contract distinguishes literal sequence matches from historical repair and accession associations. The supplemental catalogue describes 11,911 distinct coordinate contents: 11,388 newly stored contents and 523 already in historical archives. These collection totals overlap and must not be added as independent observations.

Predicted filenames can contain tcr_pmhc_hash; native filenames use PDB accessions. Use the inventory instead of constructing filenames: one sequence hash can identify several native accessions. Historical idx and complex.id are not current record IDs.

Read coordinates and evidence together

VDJdb's cdr3 fields are anchor-inclusive junctions, including conserved Cys104 and terminal Phe/Trp118. Exact junction and pMHC matching establishes file availability; it does not prove identical full variable domains or experimental constructs. Keep submitted and repaired sequence states distinct.

Native coordinates originate from experimental structures. Predicted coordinates are computed models. ranking_confidence, plddt, ptm, iptm and tcr_pmhc_iptm are supplied generator metrics, not assay outcomes. Contacts and orientation angles are computed from coordinates and inherit their uncertainty. The supplemental catalogue retains conflicting supplied metrics explicitly rather than selecting a preferred value.

Source positive/negative, pairing and validation flags do not establish binding outcomes. Use curated experimental evidence for those outcomes. Historical archive presence alone does not establish a retained specificity assignment. Withdrawn assignments are not experimentally demonstrated non-binders; low confidence describes the assignment, not coordinate quality. Modified ligands retain their literal chemistry and reviewed reasons.

The VDJdb build-output reference describes the complementary database tables. Join records and chains by record_id; keep structure links separate from the automatic structure-evidence producer's stricter acceptance rules. The dataset revision and its verification files identify the link snapshot. No structure prediction or model refitting is needed to retrieve these files.