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--- |
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viewer: false |
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license: cc-by-4.0 |
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tags: |
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- chemistry |
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- biology |
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- molecular dynamics |
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- neural network potential |
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pretty_name: 'mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics' |
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author: A. Mirarchi, T. Giorgino and G. De Fabritiis |
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size_categories: |
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- 10M<n<100M |
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--- |
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# mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics |
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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. |
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## Availability |
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- [torchmd-net dataloader](https://github.com/torchmd/torchmd-net/blob/main/torchmdnet/datasets/mdcath.py) |
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- [playmolecule](https://open.playmolecule.org/mdcath) |
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- [scripts to load, convert and rebuild](https://github.com/compsciencelab/mdCATH) |
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## Citing The Dataset |
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Please cite this manuscript for papers that use the mdCATH dataset: |
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> Mirarchi, A., Giorgino, T. & De Fabritiis, G. mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics. Sci Data 11, 1299 (2024). https://doi.org/10.1038/s41597-024-04140-z. Preprint available at [arXiv:2407.14794](https://arxiv.org/abs/2407.14794v1) (2024). |
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## Dataset Size |
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| Description | Value | |
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|:---------------------|:-------------| |
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| Domains | 5,398 | |
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| Trajectories | 134,950 | |
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| Total sampled time | 62.6 ms | |
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| Total atoms | 11,671,592 | |
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| Total amino acids | 740,813 | |
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| Avg. traj. length | 464 ns | |
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| Avg. system size | 2,162 atoms | |
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| Avg. domain length | 137 AAs | |
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| Total file size | 3.3 TB | |
