|
--- |
|
viewer: false |
|
license: cc-by-4.0 |
|
tags: |
|
- chemistry |
|
- biology |
|
- molecular dynamics |
|
- neural network potential |
|
pretty_name: 'mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics' |
|
--- |
|
|
|
|
|
# mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics |
|
|
|
This dataset comprises all-atom systems for 5,398 CATH domains, modeled with a state-of-the-art classical force field, and simulated in five replicates each at five temperatures from 320 K to 450 K. |
|
|
|
## Availability |
|
- [torchmd-net dataloader](https://github.com/torchmd/torchmd-net/blob/main/torchmdnet/datasets/mdcath.py) |
|
- [playmolecule](https://open.playmolecule.org/mdcath) |
|
- [scripts to load, convert and rebuild](https://github.com/compsciencelab/mdCATH) |
|
|
|
|
|
## Citing The Dataset |
|
Please cite this manuscript for papers that use the mdCATH dataset: |
|
|
|
> Antonio Mirarchi, Toni Giorgino, Gianni De Fabritiis. "mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics" ([arXiv:2407.14794](https://arxiv.org/abs/2407.14794v1)) |
|
|
|
## Dataset Size |
|
|
|
| Description | Value | |
|
|:---------------------|:-------------| |
|
| Domains | 5,398 | |
|
| Trajectories | 134,950 | |
|
| Total sampled time | 62.6 ms | |
|
| Total atoms | 11,671,592 | |
|
| Total amino acids | 740,813 | |
|
| Avg. traj. length | 464 ns | |
|
| Avg. system size | 2,162 atoms | |
|
| Avg. domain length | 137 AAs | |
|
| Total file size | 3.3 TB | |
|
|
|
|
