Datasets:
Update README.md
Browse filesupdate readme.md, first draft
README.md
CHANGED
|
@@ -1,3 +1,39 @@
|
|
| 1 |
-
---
|
| 2 |
-
license: cc-by-nd-4.0
|
| 3 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
license: cc-by-nd-4.0
|
| 3 |
+
tags:
|
| 4 |
+
- chemistry
|
| 5 |
+
- biology
|
| 6 |
+
- molecular dynamics
|
| 7 |
+
- neural network potential
|
| 8 |
+
---
|
| 9 |
+
|
| 10 |
+
# mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics
|
| 11 |
+
|
| 12 |
+
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 413 K.
|
| 13 |
+
|
| 14 |
+
---
|
| 15 |
+
## Availability
|
| 16 |
+
- torchmd-net dataloader
|
| 17 |
+
- playmolecule
|
| 18 |
+
- vmd script to load and analysis
|
| 19 |
+
|
| 20 |
+
---
|
| 21 |
+
## Citing The Dataset
|
| 22 |
+
Please cite this manuscript for papers that use the mdCATH dataset:
|
| 23 |
+
|
| 24 |
+
---
|
| 25 |
+
## Dataset Size
|
| 26 |
+
|
| 27 |
+
| Description | Value |
|
| 28 |
+
|:---------------------|:-------------|
|
| 29 |
+
| Domains | 5,398 |
|
| 30 |
+
| Trajectories | 134,925 |
|
| 31 |
+
| Total sampled time | 62.6 ms |
|
| 32 |
+
| Total atoms | 11,671,592 |
|
| 33 |
+
| Total amino acids | 740,813 |
|
| 34 |
+
| Avg. traj. length | 464 ns |
|
| 35 |
+
| Avg. system size | 2,162 atoms |
|
| 36 |
+
| Avg. domain length | 137 AAs |
|
| 37 |
+
| Total file size | 3.3 TB |
|
| 38 |
+
|
| 39 |
+
---
|