| --- |
| license: cc-by-4.0 |
| tags: |
| - biology |
| - proteins |
| - intrinsically-disordered-proteins |
| - molecular-dynamics |
| - Mpipi |
| - OpenMpipi |
| - trajectories |
| - BENDER |
| - IDP |
| pretty_name: BENDER MPIPI-Recharged trajectories |
| size_categories: |
| - 10K<n<100K |
| --- |
| |
| # BENDER: MPIPI-Recharged trajectories |
|
|
| Raw MPIPI-Recharged coarse-grained molecular dynamics trajectories for the |
| **10,282 intrinsically disordered proteins from 2,156 organisms** of BENDER, in six taxa |
| (mammals, plants, fungi, protists, bacteria and viruses). BENDER simulates every sequence with two independently |
| parameterized force fields. The CALVADOS-2 trajectories of the same proteins are at |
| [taseef/BENDER](https://huggingface.co/datasets/taseef/BENDER), in the same layout. |
|
|
| Each protein folder contains: |
| - `<uniprot_id>.dcd`, the MPIPI-Recharged trajectory (one bead per residue) |
| - `top.pdb`, the topology |
|
|
| ## Taxa |
|
|
| | Taxon | Sequences | Organisms | |
| |---|---|---| |
| | Bacteria | 2,858 | 654 | |
| | Plants | 2,438 | 224 | |
| | Fungi | 1,537 | 413 | |
| | Mammals | 1,361 | 155 | |
| | Viruses | 1,025 | 464 | |
| | Protists | 1,063 | 246 | |
| | **Total** | **10,282** | **2,156** | |
|
|
| ## Taxonomic composition |
|
|
|  |
|
|
| Inner ring, the six taxa. Middle ring, clades from the NCBI Taxonomy (phylum for bacteria, class for fungi, order for plants and mammals, eukaryotic supergroup for protists and family for viruses). Outer ring, organisms, with every organism of at least 45 sequences named with its sequence count. |
|
|
| ## Folder structure |
|
|
| ``` |
| <Taxon>/ |
| └── <uniprot_id>/ |
| ├── <uniprot_id>.dcd |
| └── top.pdb |
| ``` |
|
|
| ## Loading a trajectory |
|
|
| ```python |
| from huggingface_hub import hf_hub_download |
| import mdtraj as md |
| |
| dcd = hf_hub_download(repo_id="taseef/MPIPI-Recharged", filename="Bacteria/N0AZA6/N0AZA6.dcd", repo_type="dataset") |
| pdb = hf_hub_download(repo_id="taseef/MPIPI-Recharged", filename="Bacteria/N0AZA6/top.pdb", repo_type="dataset") |
| traj = md.load(dcd, top=pdb) |
| print(traj) |
| ``` |
|
|
| ## Simulation protocol |
|
|
| - Force field: MPIPI-Recharged (R. Tejedor et al., *ACS Cent. Sci.* 2025), run with OpenMpipi in OpenMM |
| - Temperature 300 K, ionic strength 150 mM, no terminal charges and no pH dependence |
| - Langevin middle integrator, friction 0.01 ps⁻¹, time step 10 fs |
| - Cubic box of side 50 nm (N ≤ 300) or ⌊N/5⌋ + 20 nm otherwise; every chain stays whole (largest bond 0.49 nm) |
| - Simulation length 100 ns for N ≤ 150 and 100·(N/150)^1.5 ns otherwise, the same budget as the CALVADOS-2 runs |
| - Frames: 10,000, 15,000 or 20,000, started from an energy-minimized self-avoiding random walk |
| - The first half of each trajectory is equilibration; all BENDER analyses use the second half |
|
|
| ## Companion resources |
|
|
| - CALVADOS-2 trajectories of the same proteins: [taseef/BENDER](https://huggingface.co/datasets/taseef/BENDER) |
| - MPIPI-GG trajectories of a 957-sequence subset, and the per-sequence properties of both MPIPI models: |
| [taseef/BENDER-MPIPI](https://huggingface.co/datasets/taseef/BENDER-MPIPI) |
| - Simulation inputs, analysis code, per-sequence tables and figure scripts: |
| [github.com/Sabian98/BENDER](https://github.com/Sabian98/BENDER) |
|
|
| ## License |
|
|
| CC BY 4.0. Free to use for any purpose, provided you cite BENDER. |
|
|
| ## Citation |
|
|
| T. Rahman, Arginine–Aromatic Attraction Divides Coarse-Grained IDP Force Fields Across the Tree of Life, submitted to the *Journal of |
| Chemical Theory and Computation* (2026). |
|
|
