Upload README.md

README.md

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+---
+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
+task_categories:
+- other
+language:
+- en
+---
+
+# 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 Cα trajectory (200 ns+)
+- `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")
+
+# Load trajectory
+traj = md.load(
+    "./trajectories/N0AZA6/N0AZA6.dcd",
+    top="./trajectories/N0AZA6/top.pdb"
+)
+print(traj)
+```
+
+---
+
+## Simulation protocol
+
+| Parameter | Value |
+|---|---|
+| Force field | CALVADOS-2 (Cα coarse-grained, Tesei & Lindorff-Larsen 2023) |
+| Ensemble | NVT, 300 K |
+| Ionic strength | 0.15 M NaCl |
+| Minimum length | 200 ns |
+| Long sequences (>150 res) | Extended — length scaled to residues^1.5 |
+| Equilibration | First 50 % of each trajectory discarded |
+| Clustering | Global CD-HIT at 90 % sequence identity across all kingdoms |
+| Scope | Pure complete IDPs only — no IDR fragments, no domain context |
+| Convergence | 87.4 % of sequences exceed ν fit R² ≥ 0.99 |
+
+---
+
+## Prediction targets
+
+10 ensemble-level targets per sequence:
+
+**Geometric properties**
+
+| Target | Description |
+|---|---|
+| `Rg` | Radius of gyration |
+| `Re` | End-to-end distance |
+| `nu` | Flory scaling exponent |
+| `delta` | Asphericity |
+| `A0` | Flory prefactor |
+
+**Contact network properties**
+
+| Target | Description |
+|---|---|
+| `global_efficiency` | Global network efficiency |
+| `fragmentation_index` | Fragmentation index |
+| `avg_clustering` | Average clustering coefficient |
+| `transitivity` | Network transitivity |
+| `degree_assortativity` | Degree assortativity |
+
+---
+
+## Companion resources
+
+- **Feature dataset** (80+ computed features per protein):
+  [`taseef/BENDER-features`](https://huggingface.co/datasets/taseef/BENDER-features)
+- **KESTREL model** (sequence → 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](https://creativecommons.org/licenses/by/4.0/) — free to use for any purpose with attribution.
+
+*BENDER: making IDPs go supersonic.*