taseef/BENDER_SAMPLE

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

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

@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.