Datasets:
Update README.md
Browse files
README.md
CHANGED
@@ -26,4 +26,78 @@ configs:
|
|
26 |
path: data/valid-*
|
27 |
- split: test
|
28 |
path: data/test-*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
29 |
---
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
26 |
path: data/valid-*
|
27 |
- split: test
|
28 |
path: data/test-*
|
29 |
+
license: apache-2.0
|
30 |
+
task_categories:
|
31 |
+
- token-classification
|
32 |
+
tags:
|
33 |
+
- chemistry
|
34 |
+
- biology
|
35 |
+
size_categories:
|
36 |
+
- 10K<n<100K
|
37 |
---
|
38 |
+
|
39 |
+
|
40 |
+
# Dataset Card for Stability Stability Dataset
|
41 |
+
|
42 |
+
### Dataset Summary
|
43 |
+
|
44 |
+
The Stability Stability task is to predict the concentration of protease at which a protein can retain its folded state. Protease, being integral to numerous biological processes, bears significant relevance and a profound comprehension of protein stability during protease interaction can offer immense value, especially in the creation of novel therapeutics.
|
45 |
+
|
46 |
+
## Dataset Structure
|
47 |
+
|
48 |
+
### Data Instances
|
49 |
+
For each instance, there is a string representing the protein sequence and a float number indicating the stability score. See the [stability prediction dataset viewer](https://huggingface.co/datasets/Bo1015/stability_prediction/viewer) to explore more examples.
|
50 |
+
|
51 |
+
```
|
52 |
+
{'seq':'MEHVIDNFDNIDKCLKCGKPIKVVKLKYIKKKIENIPNSHLINFKYCSKCKRENVIENL'
|
53 |
+
'label':0.17}
|
54 |
+
```
|
55 |
+
|
56 |
+
The average for the `seq` and the `label` are provided below:
|
57 |
+
|
58 |
+
| Feature | Mean Count |
|
59 |
+
| ---------- | ---------------- |
|
60 |
+
| seq | 45 |
|
61 |
+
| label | 0.34 |
|
62 |
+
|
63 |
+
|
64 |
+
|
65 |
+
### Data Fields
|
66 |
+
|
67 |
+
- `seq`: a string containing the protein sequence
|
68 |
+
- `label`: a float number indicating the stability score of each sequence.
|
69 |
+
|
70 |
+
### Data Splits
|
71 |
+
|
72 |
+
The secondary structure prediction dataset has 3 splits: _train_, _valid_, and _test_. Below are the statistics of the dataset.
|
73 |
+
|
74 |
+
| Dataset Split | Number of Instances in Split |
|
75 |
+
| ------------- | ------------------------------------------- |
|
76 |
+
| Train | 53,614 |
|
77 |
+
| Valid | 2,512 |
|
78 |
+
| Test | 12,851 |
|
79 |
+
|
80 |
+
### Source Data
|
81 |
+
|
82 |
+
#### Initial Data Collection and Normalization
|
83 |
+
|
84 |
+
The dataset applied in this task is initially sourced from [Rocklin et al](https://www.science.org/doi/10.1126/science.aan0693) and subsequently collected within the [TAPE](https://github.com/songlab-cal/tape).
|
85 |
+
|
86 |
+
### Licensing Information
|
87 |
+
|
88 |
+
The dataset is released under the [Apache-2.0 License](http://www.apache.org/licenses/LICENSE-2.0).
|
89 |
+
|
90 |
+
### Citation
|
91 |
+
If you find our work useful, please consider citing the following paper:
|
92 |
+
|
93 |
+
```
|
94 |
+
@misc{chen2024xtrimopglm,
|
95 |
+
title={xTrimoPGLM: unified 100B-scale pre-trained transformer for deciphering the language of protein},
|
96 |
+
author={Chen, Bo and Cheng, Xingyi and Li, Pan and Geng, Yangli-ao and Gong, Jing and Li, Shen and Bei, Zhilei and Tan, Xu and Wang, Boyan and Zeng, Xin and others},
|
97 |
+
year={2024},
|
98 |
+
eprint={2401.06199},
|
99 |
+
archivePrefix={arXiv},
|
100 |
+
primaryClass={cs.CL},
|
101 |
+
note={arXiv preprint arXiv:2401.06199}
|
102 |
+
}
|
103 |
+
```
|