根据基因名批量查询下载PDB蛋白结构数据库

 

下载Using EntrezDirect as noted to get structure accessions

https://www.ncbi.nlm.nih.gov/books/NBK179288/

 

for i in `cat all.epi.regulators.txt`
do
echo $i
esearch -db structure -query "$i [GENE]" | esummary | xtract -pattern DocumentSummary -element PdbAcc,ExpMethod,Resolution,PdbClass,PdbDepositDate,PdbDescr,string > $i.pdb_id
done

 

偶尔会有网络连接问题

最后再下一遍

ls *.pdb_id | sed "s/.pdb_id//" > downloaded.list

grep -vxFf downloaded.list all.epi.regulators.txt

　　

 

参考：

  • http://localhost:17449/lab/tree/projects/LiLab/selfDB/Drug-DB/Drug_to_gene.ipynb
  • ~/projects/LiLab/selfDB/rcsb_PDB/
  • https://www.biostars.org/p/9576260/

 

posted @ 2024-12-13 05:39  Life·Intelligence  阅读(19)  评论(0)  编辑  收藏  举报
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