| --- |
| license: mit |
| tags: |
| - protein |
| - structural-biology |
| - thermodynamic-stability |
| --- |
| |
| # DeepEF Datasets |
|
|
| Protein structure datasets used for training and evaluating [DeepEF](https://github.com/shaharec/DeepEF) — |
| a deep learning framework for predicting protein thermodynamic stability. |
|
|
| ## Contents |
|
|
| | Path | Size | Description | |
| |------|------|-------------| |
| | `casp12_data_30/` | ~110GB | CASP12 structures with ProtT5 embeddings; per-protein `.pt` tensors split into train/test/valid-* | |
| | `Processed_K50_dG_datasets/` | ~2.2GB | K50 ddG mutation datasets with AlphaFold PDB models | |
| | `megascale_proteins.csv` | small | Megascale protein list | |
|
|
| ## Data Format (casp12_data_30) |
|
|
| Each protein is a folder under `train/`, `test/`, or `valid-*/`: |
| ``` |
| PROTEIN_ID/ |
| ├── crd_backbone.pt # Backbone coordinates [seq_len, 4, 3] |
| ├── ang.pt # Dihedral angles |
| ├── mask.pt # Valid residue mask |
| ├── seq_one_hot.pt # One-hot amino acid encoding [seq_len, 20] |
| ├── seq.pt # Raw sequence string |
| ├── seq_mut.pt # Mutant sequence string |
| ├── proT5_emb.pt # ProtT5 embeddings [seq_len, 1024] |
| ├── proT5_emb_cycle1-4.pt # Cyclic permutation embeddings |
| └── proT5_emb_mut.pt # Mutant ProtT5 embeddings |
| ``` |
|
|
| ## Usage |
|
|
| ```python |
| from huggingface_hub import snapshot_download, hf_hub_download |
| import torch |
| |
| # Download a single protein |
| path = hf_hub_download( |
| repo_id="shaharec/deepef-data", |
| repo_type="dataset", |
| filename="casp12_data_30/train/1A0C_1_A/crd_backbone.pt", |
| ) |
| coords = torch.load(path) |
| |
| # Download an entire split (large!) |
| snapshot_download( |
| repo_id="shaharec/deepef-data", |
| repo_type="dataset", |
| allow_patterns="casp12_data_30/train/*", |
| local_dir="./data", |
| ) |
| ``` |
|
|
