electricsheepafrica/APED-African-Protein-Engineering-Dataset

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).

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

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

@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