Datasets:
| # APED Pipeline Configuration | |
| # For reproducibility of results | |
| # Dataset Parameters | |
| dataset: | |
| name: "APED-Thermophile-Module" | |
| version: "1.0.0" | |
| # Data Sources | |
| sources: | |
| alphafold_db: "https://alphafold.ebi.ac.uk" | |
| uniprot: "https://www.uniprot.org" | |
| # Organism Taxonomy IDs (UniProt) | |
| organisms: | |
| - name: "Thermus thermophilus" | |
| taxonomy_id: 274 | |
| - name: "Thermococcus kodakarensis" | |
| taxonomy_id: 69014 | |
| - name: "Sulfolobus solfataricus" | |
| taxonomy_id: 2287 | |
| - name: "Pyrococcus furiosus" | |
| taxonomy_id: 2261 | |
| # Feature Extraction Parameters | |
| features: | |
| structural: | |
| - mean_plddt | |
| - helix_fraction | |
| - sheet_fraction | |
| - coil_fraction | |
| sequence: | |
| - sequence_length | |
| - molecular_weight | |
| - isoelectric_point | |
| - instability_index | |
| - aromaticity | |
| - hydrophobicity | |
| - charge | |
| # RFdiffusion Parameters | |
| rfdiffusion: | |
| colab_notebook: "https://colab.research.google.com/github/sokrypton/ColabDesign/blob/main/rf/examples/diffusion.ipynb" | |
| parameters: | |
| contigs: "A1-50/50-100" | |
| iterations: 50 | |
| num_designs: 5 | |
| symmetry: "none" | |
| use_beta_model: false | |
| # ProteinMPNN Parameters | |
| proteinmpnn: | |
| sequences_per_backbone: 8 | |
| sampling_temperature: 0.1 | |
| # Validation Thresholds | |
| validation: | |
| min_plddt: 90.0 | |
| max_rmsd: 1.0 | |
| min_ptm: 0.7 | |
| # Output | |
| output: | |
| huggingface_repo: "electricsheepafrica/APED-African-Protein-Engineering-Dataset" | |
| formats: | |
| - parquet | |
| - fasta | |
| - csv | |