https://github.com/zyxue/pdb-secondary-structure
Transform data from RCSB Protein Data Bank for secondary structure prediction
https://github.com/zyxue/pdb-secondary-structure
machine-learning prediction protein protein-secondary
Last synced: 10 months ago
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Transform data from RCSB Protein Data Bank for secondary structure prediction
- Host: GitHub
- URL: https://github.com/zyxue/pdb-secondary-structure
- Owner: zyxue
- Created: 2018-06-06T21:14:18.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2019-02-20T18:24:51.000Z (over 7 years ago)
- Last Synced: 2025-05-07T07:39:36.898Z (about 1 year ago)
- Topics: machine-learning, prediction, protein, protein-secondary
- Language: Jupyter Notebook
- Homepage:
- Size: 103 MB
- Stars: 12
- Watchers: 3
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
This repo records details of how the protein secondary structure data is curated.
#### Download secondary structure data
```
DATE_STAMP=$(date +'%Y-%m-%d')
wget https://cdn.rcsb.org/etl/kabschSander/ss.txt.gz -O ${DATE_STAMP}-ss.txt.gz
```
#### Transform to csv format
```
python transform_ss_txt_to_csv.py -i ${DATE_STAMP}-ss.txt.gz
```
#### Download PISCES data, removed peptides with high similarity
https://academic.oup.com/bioinformatics/article/19/12/1589/258419
```
wget http://dunbrack.fccc.edu/Guoli/culledpdb_hh/cullpdb_pc25_res2.0_R0.25_d180531_chains9099.gz
```
If the above URL doesn't work, update it according to http://dunbrack.fccc.edu/Guoli/culledpdb_hh/.
Interpretation of the filename based on http://dunbrack.fccc.edu/Guoli/pisces_download.php:
* `pc25`: the percentage identity cutoff is 25%
* `res2.0`: he resolution cutoff is 2.0 angstroms
* `R0.25`: the R-factor cutoff is 0.25
* `d180531`: datestamp
* `chains9099`: the number of sequences in the file
In addition:
* `inclNOTXRAY`: include sequences from non-xray-derived structures (mostly NMR but also including electron diffraction, FTIR, fiber diffraction, etc.).
* `inclCA`: include sequences of structures that contain only backbone CA coordinates.
#### Related Kaggle page:
https://www.kaggle.com/alfrandom/protein-secondary-structure