{"id":17652285,"url":"https://github.com/zyxue/pdb-secondary-structure","last_synced_at":"2025-09-03T03:40:00.420Z","repository":{"id":141946233,"uuid":"136386765","full_name":"zyxue/pdb-secondary-structure","owner":"zyxue","description":"Transform data from RCSB Protein Data Bank for secondary structure prediction","archived":false,"fork":false,"pushed_at":"2019-02-20T18:24:51.000Z","size":107743,"stargazers_count":12,"open_issues_count":0,"forks_count":5,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-05-07T07:39:36.898Z","etag":null,"topics":["machine-learning","prediction","protein","protein-secondary"],"latest_commit_sha":null,"homepage":"","language":"Jupyter 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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"This repo records details of how the protein secondary structure data is curated.\n\n\n#### Download secondary structure data\n\n```\nDATE_STAMP=$(date  +'%Y-%m-%d')\nwget https://cdn.rcsb.org/etl/kabschSander/ss.txt.gz -O ${DATE_STAMP}-ss.txt.gz\n```\n\n#### Transform to csv format\n```\npython transform_ss_txt_to_csv.py -i ${DATE_STAMP}-ss.txt.gz\n```\n\n#### Download PISCES data, removed peptides with high similarity\n\nhttps://academic.oup.com/bioinformatics/article/19/12/1589/258419\n\n```\nwget http://dunbrack.fccc.edu/Guoli/culledpdb_hh/cullpdb_pc25_res2.0_R0.25_d180531_chains9099.gz\n```\n\nIf the above URL doesn't work, update it according to http://dunbrack.fccc.edu/Guoli/culledpdb_hh/.\n\nInterpretation of the filename based on http://dunbrack.fccc.edu/Guoli/pisces_download.php: \n\n* `pc25`:  the percentage identity cutoff is 25%\n* `res2.0`: he resolution cutoff is 2.0 angstroms\n* `R0.25`: the R-factor cutoff is 0.25\n* `d180531`: datestamp\n* `chains9099`: the number of sequences in the file\n\nIn addition:\n\n* `inclNOTXRAY`: include sequences from non-xray-derived structures (mostly NMR but also including electron diffraction, FTIR, fiber diffraction, etc.). \n* `inclCA`: include sequences of structures that contain only backbone CA coordinates.\n\n#### Related Kaggle page:\n\nhttps://www.kaggle.com/alfrandom/protein-secondary-structure\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzyxue%2Fpdb-secondary-structure","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzyxue%2Fpdb-secondary-structure","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzyxue%2Fpdb-secondary-structure/lists"}