k-fold-structure/repsp-benchmark

K-Fold Structure Benchmark (AFDB-Multimer)

Everything needed to run the folding / co-folding / probing benchmarks except per-encoder features (which you extract from k-fold-structure/repsp-triprorep-tokens with your encoder, see the GitHub release README).

The benchmark goes apo → holo: predict properties of the bound homodimer ("holo") from the unbound monomer ("apo"). The two chains are identical (homodimer), so each residue position carries a single label.

Contents

splits/
    folding/{train,valid,test}.txt        # 390,627 / 400 / 1,000 PIDs (cluster reps, LMDB-cleaned)
    probing/splits_{train,valid,test}.txt # 39,076 / 400 / 1,000 PIDs (10% of folding train)
probing/
    labels.pkl                            # per-residue labels: binding_site / delta_sasa_mean / levy_tier / bond_type_plip
boltz_apo_tokens/   shard*.tar            # Boltz-tokenized apo monomers (folding input)
boltz_apo_targets/  shard*.tar            # apo structure targets
boltz_holo_tokens/  shard*.tar            # Boltz-tokenized holo dimers (co-folding input)
boltz_holo_targets/ shard*.tar            # holo structure targets

Each boltz_* dir is split into ~5 GB tar shards (the native dirs hold ~395k small files each, too many to upload individually). Extract all shards of a dir into one folder:

hf download k-fold-structure/repsp-benchmark --repo-type dataset \
    --include "boltz_holo_tokens/*" --local-dir ./benchmark
cd ./benchmark/boltz_holo_tokens
for t in shard*.tar; do tar xf "$t"; done && rm shard*.tar
# -> manifest.json  records/*.json  tokens/*.pkl

Note on "Boltz": the boltz_* dirs use the tokenized layout the folding trunk (SimpleFold) reads, manifest.json + records/ + tokens/ (or structures/ for targets). After extracting, point the folding datamodule's tokenized_dir / target_dir at these folders.

Notes

• Splits are LMDB-cleaned: ~0.06% of train PIDs that failed tokenization are already removed, so you won't hit KeyErrors.
• The folding symmetries config field is unused for this protein-only benchmark (no ligands, chain A<->B symmetry is computed on-the-fly).

License

MIT