Add Cryptic-Binding dataset
Browse files
Cryptic-Binding/README.md
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# Cryptic-Binding
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Cryptic protein binding sites from CryptoBank + apo-holo pair mining.
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Filtered for CDR3 compatibility and NMA open-state stability, then
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clustered by Zernike pocket-shape descriptors.
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## Files
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- `cryptic_sites_final.csv` (1990 rows) - all surviving sites
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- `cryptic_sites_centroids.csv` (1 rows) - one per cluster
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- `farm_report.md` - filter funnel + top sites
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**Evidence:** experimental=1990, computational=0
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## Columns
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`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`
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## Usage
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```python
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import pandas as pd
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from huggingface_hub import hf_hub_download
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path = hf_hub_download('Nanoflow/nanoflow-data', 'Cryptic-Binding/cryptic_sites_centroids.csv',
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repo_type='dataset')
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df = pd.read_csv(path)
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```
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Structures are referenced by PDB ID; download from RCSB as needed.
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Cryptic-Binding/cryptic_sites_centroids.csv
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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
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cb_5SMF_D_15a8d0c9,5SMF,P0DTD1,D,cryptobank,experimental,0.34,757.8,14.74,8.18,0.444,0.474,0.4,1,0.0,1.0,"crypticity=True, ligand=K1S"
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Cryptic-Binding/cryptic_sites_final.csv
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The diff for this file is too large to render.
See raw diff
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Cryptic-Binding/farm_report.md
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# Cryptic Site Farming Report
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**Total sites passing all filters:** 1990
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**Non-redundant centroid set:** 1
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## Top 20 Sites by Compatibility Score
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| site_id | pdb_id | source | evidence_tier | asa_a2 | depth_a | compatibility_score | cluster_id |
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|:-------------------|:---------|:-----------|:----------------|---------:|----------:|----------------------:|-------------:|
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| cb_4Q3K_B_62e98b95 | 4Q3K | cryptobank | experimental | 652.7 | 11.44 | 0.906 | 0 |
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| cb_5S7X_A_3a583cf2 | 5S7X | cryptobank | experimental | 616.9 | 11.56 | 0.879 | 0 |
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| cb_6P13_B_28adc879 | 6P13 | cryptobank | experimental | 583.8 | 11.24 | 0.873 | 0 |
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| cb_4AHA_A_a426f496 | 4AHA | cryptobank | experimental | 678.4 | 11.56 | 0.867 | 0 |
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| cb_4AGI_B_91130f66 | 4AGI | cryptobank | experimental | 678.4 | 11.56 | 0.866 | 0 |
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| cb_4AGI_C_ddeb11df | 4AGI | cryptobank | experimental | 678.4 | 11.54 | 0.866 | 0 |
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| cb_4AGT_B_00722b68 | 4AGT | cryptobank | experimental | 678.4 | 11.55 | 0.865 | 0 |
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| cb_7FOR_A_21480745 | 7FOR | cryptobank | experimental | 652.2 | 11.3 | 0.863 | 0 |
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| cb_6BQX_A_2df7288c | 6BQX | cryptobank | experimental | 575.5 | 11.83 | 0.863 | 0 |
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| cb_8OSN_A_0d6a35a4 | 8OSN | cryptobank | experimental | 607.7 | 11.5 | 0.86 | 0 |
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| cb_3R6T_A_2fc24939 | 3R6T | cryptobank | experimental | 648.5 | 12 | 0.857 | 0 |
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| cb_3Q3O_B_726e82ed | 3Q3O | cryptobank | experimental | 615.9 | 11.56 | 0.857 | 0 |
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| cb_4JWS_B_9432b458 | 4JWS | cryptobank | experimental | 648.1 | 11.77 | 0.856 | 0 |
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| cb_4AHA_B_f7c27604 | 4AHA | cryptobank | experimental | 678.4 | 11.76 | 0.85 | 0 |
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| cb_4C1Y_A_745e9fcc | 4C1Y | cryptobank | experimental | 697.3 | 11.47 | 0.846 | 0 |
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| cb_7ZH8_C_12fcbe21 | 7ZH8 | cryptobank | experimental | 623.9 | 11.16 | 0.845 | 0 |
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| cb_5RYH_A_cd2cea5c | 5RYH | cryptobank | experimental | 656.9 | 11.12 | 0.831 | 0 |
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| cb_3HV6_A_94e0dce1 | 3HV6 | cryptobank | experimental | 693.3 | 11.67 | 0.825 | 0 |
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| cb_8ELZ_A_cd2b5eb0 | 8ELZ | cryptobank | experimental | 623 | 11.77 | 0.824 | 0 |
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| cb_7VCP_A_2be6014f | 7VCP | cryptobank | experimental | 606.3 | 11.71 | 0.824 | 0 |
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## Usage
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Load `cryptic_sites_centroids.csv` as the training corpus for the
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RL policy in Step 5. Each row is one non-redundant cryptic site.
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