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Algae.zip

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Archaea.zip

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Bacteria.zip

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Fungi.zip

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Insects.zip

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Mammals.zip

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Nematodes.zip

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Other invertebrates.zip

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Other vertebrates.zip

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Other.zip

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Other_invertebrates.zip

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Other_vertebrates.zip

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Parasites_Protists.zip

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Plants.zip

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README.md

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----
-license: cc-by-4.0
----
+
+```markdown
+---
+license: cc-by-4.0
+tags:
+- biology
+- proteins
+- intrinsically-disordered-proteins
+- molecular-dynamics
+- CALVADOS
+- trajectories
+- BENDER
+- IDP
+pretty_name: BENDER — Biological ENsembles of Disordered proteins across kingdoms
+size_categories:
+- 10K<n<100K
+---
+
+# BENDER — Biological ENsembles of Disordered proteins across kingdoms
+
+Raw CALVADOS coarse-grained molecular dynamics trajectories for 
+**11,533 intrinsically disordered proteins** spanning 13 kingdoms of life.
+
+Each protein folder contains:
+- `<uniprot_id>.dcd` — CALVADOS Ca trajectory (200ns+)
+- `top.pdb` — topology file
+
+## Folder structure
+
+```
+Kingdom.zip/
+└── <uniprot_id>/
+    ├── <uniprot_id>.dcd
+    └── top.pdb
+```
+
+## Available zip files
+
+| File | Kingdom | Sequences |
+|---|---|---|
+| Bacteria.zip | Bacteria | 2,850 |
+| Plants.zip | Plants | 2,480 |
+| Fungi.zip | Fungi | 1,507 |
+| Mammals.zip | Mammals | 1,361 |
+| Parasites_Protists.zip | Parasites/Protists | 1,049 |
+| Viruses.zip | Viruses | 1,025 |
+| Other_Vertebrates.zip | Other vertebrates | 711 |
+| Insects.zip | Insects | 289 |
+| Nematodes.zip | Nematodes | 95 |
+| Other_Invertebrates.zip | Other invertebrates | 77 |
+| Archaea.zip | Archaea | 76 |
+| Algae.zip | Algae | 10 |
+
+## Loading a trajectory
+
+```python
+from huggingface_hub import hf_hub_download
+import mdtraj as md
+import zipfile
+
+# Download zipped kingdom
+zip_path = hf_hub_download(
+    repo_id="taseef/BENDER",
+    filename="Bacteria.zip",
+    repo_type="dataset"
+)
+
+# Extract specific protein
+with zipfile.ZipFile(zip_path, 'r') as z:
+    z.extract("N0AZA6/N0AZA6.dcd", path="./trajectories")
+    z.extract("N0AZA6/top.pdb", path="./trajectories")
+
+traj = md.load(
+    "./trajectories/N0AZA6/N0AZA6.dcd",
+    top="./trajectories/N0AZA6/top.pdb"
+)
+print(traj)
+```
+
+## Simulation protocol
+
+- Force field: CALVADOS-2 (Ca coarse-grained, Tesei & Lindorff-Larsen 2023)
+- Temperature: 300K, NVT ensemble
+- Ionic strength: 0.15M NaCl
+- Minimum simulation length: 200ns
+- Sequences >150 residues: extended simulation scaled to length^1.5
+- First 50% of trajectory discarded as equilibration
+- Global CD-HIT clustering at 90% sequence identity across all kingdoms
+- Pure complete IDPs only — no IDR fragments, no domain context
+- 87.4% of sequences exceed nu_fit_r2 >= 0.99 convergence threshold
+
+## Prediction targets
+
+10 ensemble-level targets per sequence:
+
+**Geometric properties**
+- Rg — radius of gyration
+- Re — end-to-end distance
+- nu — Flory scaling exponent
+- delta — asphericity
+- A0 — Flory prefactor
+
+**Contact network properties**
+- global_efficiency
+- fragmentation_index
+- avg_clustering
+- transitivity
+- degree_assortativity
+
+## Companion resources
+
+- Feature dataset (80+ computed features per protein):
+  [taseef/BENDER-features](https://huggingface.co/datasets/taseef/BENDER-features)
+- KESTREL model (sequence to ensemble property predictor):
+  [taseef/KESTREL](https://huggingface.co/taseef/KESTREL)
+
+## Citation
+
+```bibtex
+@dataset{bender2026,
+  title  = {BENDER: Biological ENsembles of Disordered proteins 
+            across kingdoms},
+  year   = {2026},
+  url    = {https://huggingface.co/datasets/taseef/BENDER}
+}
+```
+
+## License
+
+CC BY 4.0 — free to use for any purpose with attribution.
+
+*BENDER: making IDPs go supersonic.*
+```

Viruses.zip

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