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license: cc-by-4.0
tags:
- biology
- proteins
- intrinsically-disordered-proteins
- molecular-dynamics
- CALVADOS
- trajectories
- BENDER
- IDP
pretty_name: BENDER Sample — Biological ENsembles of Disordered proteins across taxa
size_categories:
- n<1K
---
# BENDER Sample — Biological ENsembles of Disordered proteins across taxa
A representative sample of CALVADOS coarse-grained molecular dynamics
trajectories from the full BENDER dataset, comprising sequences across
8 taxonomic groups.
Each protein folder contains:
- `<uniprot_id>.dcd` — CALVADOS Ca trajectory (200ns+)
- `top.pdb` — topology file
## Folder structure
```
TaxonomicGroup/
└── <uniprot_id>/
├── <uniprot_id>.dcd
└── top.pdb
```
## Sample composition
| Taxonomic Group | Sequences |
|---|---|
| Bacteria | 60 |
| Plants | 54 |
| Fungi | 31 |
| Mammals | 28 |
| Viruses | 22 |
| Insects | 6 |
| Nematodes | 2 |
| Archaea | 2 |
| Algae | 2 |
| Other | 2 |
## Loading a trajectory
```python
from huggingface_hub import hf_hub_download
import mdtraj as md
import zipfile
dcd = hf_hub_download(
repo_id="taseef/BENDER-sample",
filename="Bacteria/Q167T1/Q167T1.dcd",
repo_type="dataset"
)
pdb = hf_hub_download(
repo_id="taseef/BENDER-sample",
filename="Bacteria/Q167T1/top.pdb",
repo_type="dataset"
)
traj = md.load(dcd, 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
- First 50% discarded as equilibration
- Global CD-HIT clustering at 90% sequence identity across all taxa
## Citation
```bibtex
@misc{taseef_2026,
author = { taseef },
title = { BENDER_SAMPLE (Revision 6ebf2bc) },
year = 2026,
url = { https://huggingface.co/datasets/taseef/BENDER_SAMPLE },
doi = { 10.57967/hf/8678 },
publisher = { Hugging Face }
}
```
## License
CC BY 4.0 — free to use with attribution.
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