---
license: mit
task_categories:
  - feature-extraction
language:
  - en
tags:
  - biology
  - proteins
  - thermophiles
  - protein-engineering
  - alphafold
  - africa
size_categories:
  - n<1K
---

# APED: African Protein Engineering Dataset - Thermophile Module

A curated dataset of protein structures from African thermophilic organisms, designed for machine learning applications in protein engineering and heat-stable biologic design.

## Mission

Enable African researchers to computationally design **heat-stable biologics** (vaccines, insulin, diagnostics) that survive supply chains without cold storage.

## Dataset Contents

### Thermophile Protein Features

| File | Description |
|------|-------------|
| `data/aped_ml_dataset.parquet` | 500 proteins with 19 ML-ready features |
| `designs/best_designs.fasta` | 3 novel protein designs (pLDDT > 90%) |
| `designs/mpnn_results.csv` | Full design candidates (40 sequences) |

### Source Organisms

Proteins from thermophilic organisms found in African extreme environments:
- Ethiopian hot springs
- Lake Magadi, Kenya
- Lac Abbé, Djibouti
- Algerian thermal springs

### Features (19 total)

| Feature | Description |
|---------|-------------|
| `uniprot_id` | UniProt accession |
| `organism` | Source organism |
| `sequence` | Amino acid sequence |
| `sequence_length` | Number of residues |
| `mean_plddt` | AlphaFold confidence (0-100) |
| `helix_fraction` | α-helix content |
| `sheet_fraction` | β-sheet content |
| `coil_fraction` | Coil content |
| `hydrophobicity` | Mean hydrophobicity |
| `charge` | Net charge at pH 7 |
| `molecular_weight` | Molecular weight (Da) |
| `isoelectric_point` | Predicted pI |
| `instability_index` | Sequence instability metric |
| `aromaticity` | Aromatic residue fraction |

### Statistics

- **981** AlphaFold structures downloaded
- **500** proteins with full feature extraction
- **3** novel designs with pLDDT > 90%

## Novel Protein Designs

We generated novel thermostable protein backbones using the RFdiffusion → ProteinMPNN → AlphaFold pipeline (based on [Zheng et al., Nature Chemistry 2025](https://doi.org/10.1038/s41557-025-01998-3)).

**Top 3 Designs:**

| Design | pLDDT | RMSD | Status |
|--------|-------|------|--------|
| design3_seq4 | 91.9% | 0.74Å | Ready for synthesis |
| design3_seq7 | 91.1% | 0.58Å | Ready for synthesis |
| design3_seq2 | 90.9% | 0.69Å | Ready for synthesis |

## Usage

```python
from datasets import load_dataset
import pandas as pd

# Load dataset
dataset = load_dataset("electricsheepafrica/APED-African-Protein-Engineering-Dataset")

# Or load parquet directly
df = pd.read_parquet("hf://datasets/electricsheepafrica/APED-African-Protein-Engineering-Dataset/data/aped_ml_dataset.parquet")
```

## Future Work

�� **Coming Soon: Pathogen Module**
- *Plasmodium falciparum* (malaria) - African strains
- *Mycobacterium africanum* (TB)
- HIV-1 subtype C variants
- Application: Structure-based drug design for regional variants

## Citation

```bibtex
@dataset{aped2024,
  title={APED: African Protein Engineering Dataset - Thermophile Module},
  author={Electric Sheep Africa},
  year={2024},
  publisher={HuggingFace},
  url={https://huggingface.co/datasets/electricsheepafrica/APED-African-Protein-Engineering-Dataset}
}
```

## License

MIT License

## Contact

[Electric Sheep Africa](https://huggingface.co/electricsheepafrica)