---
license: cc-by-4.0
viewer: false
tags:
- biology
- protein-structure
- inverse-folding
- binding-site-prediction
size_categories:
- 10K<n<100K
---

# E3former Datasets

Processed datasets for *Energy-Adaptive Equivariant State Space Models for
Noise-Robust Protein Structure Representation*.

## Datasets

| Dataset | Structure | Task | Train | Validation | Test |
|---|---|---|---:|---:|---:|
| [CATH](datasets/cath/README.md) | Experimental | Inverse folding | 18,009 | 607 | 1,119 |
| [CATH-AF](datasets/cath/README.md) | AlphaFold-derived | Inverse folding | 16,467 | 559 | 1,015 |
| [PPBS](datasets/ppbs/README.md) | Experimental | Binding-site prediction | 12,577 | 3,178 | 3,984 |
| [PPBS-AF](datasets/ppbs/README.md) | AlphaFold-derived | Binding-site prediction | 11,345 | 2,876 | 3,636 |

The archives contain processed PyTorch/PyG protein objects and fixed
train/validation/test splits. PPBS includes the 70, homology, topology, and none
test subsets. Family-specific manifests record split counts and archive checksums.

## Download

```bash
hf download GENTEL-Lab/E3former_data --repo-type dataset --local-dir e3former_data
```

Or, from the E3former code directory:


```bash
python scripts/download.py --namespace GENTEL-Lab
e3former check-data
```

To install one dataset, add `--only cath`, `--only cath-af`, `--only ppbs`, or
`--only ppbs-af` to the download command. The script verifies SHA256 and extracts
the archives into the matching `data/` directories.

Use Python 3.10 and the dependencies pinned in the E3former installation.
These are processed inputs for the provided data loader, not raw PDB files.

## Sources

CATH uses [CATH](https://www.cathdb.info/) protein classifications and benchmark
splits. PPBS labels and evaluation subsets originate from
[ScanNet](https://github.com/jertubiana/ScanNet).
The AF variants provide AlphaFold-derived structures for the corresponding tasks.
This release uses CC BY 4.0 for our contributions. Source materials retain their original licenses; see
[THIRD_PARTY_DATA.md](THIRD_PARTY_DATA.md).

Please cite E3former and the relevant source datasets when using this release.