| # Cryptic-Binding |
|
|
| Cryptic protein binding sites from CryptoBank + apo-holo pair mining. |
| Filtered for CDR3 compatibility and NMA open-state stability, then |
| clustered by Zernike pocket-shape descriptors. |
|
|
| ## Files |
|
|
| - `cryptic_sites_final.csv` (1990 rows) - all surviving sites |
| - `cryptic_sites_centroids.csv` (1 rows) - one per cluster |
| - `farm_report.md` - filter funnel + top sites |
|
|
| **Evidence:** experimental=1990, computational=0 |
|
|
| ## Columns |
|
|
| `site_id`, `pdb_id`, `uniprot_id`, `chain`, `source`, `evidence_tier`, `pocket_volume`, `asa_a2`, `depth_a`, `width_a`, `polar_fraction`, `compatibility_score`, `nma_pocket_variance`, `open_state_stable`, `cluster_id`, `is_centroid`, `notes` |
|
|
| ## Usage |
|
|
| ```python |
| import pandas as pd |
| from huggingface_hub import hf_hub_download |
| |
| path = hf_hub_download('Nanoflow/nanoflow-data', 'Cryptic-Binding/cryptic_sites_centroids.csv', |
| repo_type='dataset') |
| df = pd.read_csv(path) |
| ``` |
|
|
| Structures are referenced by PDB ID; download from RCSB as needed. |
