readme.md

---
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

## Full dataset

The complete BENDER dataset (11,533 sequences) is available at:
[taseef/BENDER](https://huggingface.co/datasets/taseef/BENDER)

## Citation

```bibtex
@dataset{bender2026,
  title  = {BENDER: Biological ENsembles of Disordered proteins 
            across taxa},
  author = {Rahman, Taseef},
  year   = {2026},
  url    = {https://huggingface.co/datasets/taseef/BENDER}
}
```

## License

CC BY 4.0 — free to use with attribution.