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README.md

@@ -10,17 +10,36 @@ tags:
   - thermophiles
   - protein-engineering
   - alphafold
+  - africa
 size_categories:
   - n<1K
 ---
 
-# 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.
+A curated dataset of protein structures from African thermophilic organisms, designed for machine learning applications in protein engineering and heat-stable biologic design.
 
-## Dataset Description
+## Mission
 
-This dataset contains structural and sequence features extracted from AlphaFold-predicted structures of proteins from thermophilic organisms found in African extreme environments (hot springs, volcanic regions).
+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)
 
@@ -30,7 +49,7 @@ This dataset contains structural and sequence features extracted from AlphaFold-
 | `organism` | Source organism |
 | `sequence` | Amino acid sequence |
 | `sequence_length` | Number of residues |
-| `mean_plddt` | Mean AlphaFold confidence |
+| `mean_plddt` | AlphaFold confidence (0-100) |
 | `helix_fraction` | α-helix content |
 | `sheet_fraction` | β-sheet content |
 | `coil_fraction` | Coil content |
@@ -38,45 +57,64 @@ This dataset contains structural and sequence features extracted from AlphaFold-
 | `charge` | Net charge at pH 7 |
 | `molecular_weight` | Molecular weight (Da) |
 | `isoelectric_point` | Predicted pI |
-| `instability_index` | Sequence instability |
+| `instability_index` | Sequence instability metric |
 | `aromaticity` | Aromatic residue fraction |
-| And more... | |
 
 ### Statistics
 
-- **500 proteins** with full features
-- **981 AlphaFold structures** downloaded
-- **3 novel designs** with pLDDT > 90%
+- **981** AlphaFold structures downloaded
+- **500** proteins with full feature extraction
+- **3** novel designs with pLDDT > 90%
 
 ## Novel Protein Designs
 
-Included are 3 computationally designed proteins generated using:
-1. **RFdiffusion** - backbone generation
-2. **ProteinMPNN** - sequence design  
-3. **AlphaFold** - structure validation
+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:**
 
-Best design: **91.9% pLDDT, 0.74Å RMSD**
+| 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
 
-If you use this dataset, please cite:
-```
+```bibtex
 @dataset{aped2024,
-  title={APED: African Protein Engineering Dataset},
+  title={APED: African Protein Engineering Dataset - Thermophile Module},
   author={Electric Sheep Africa},
   year={2024},
-  publisher={HuggingFace}
+  publisher={HuggingFace},
+  url={https://huggingface.co/datasets/electricsheepafrica/APED-African-Protein-Engineering-Dataset}
 }
 ```
 
 ## License
 
 MIT License
+
+## Contact
+
+[Electric Sheep Africa](https://huggingface.co/electricsheepafrica)