Cryptic-Binding/README.md

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

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.