D3Pockets

Pockets generation

  • [zqchen@DDB S_protein]$ python27ana $D3Pockets_UCB_HOME/PyPocket_Detect.py -r fixed.pdb
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  • [zqchen@DDB S_protein]$ python27ana $D3Pockets_UCB_HOME/gensinglePDBpml.py  fixed.pdb
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  • [zqchen@DDB S_protein]$ python27ana $D3Pockets_UCB_HOME/pml2pse.py fixed_pkts.pml result.pse

D3pockets Descriptors

在D3Pockets_Descriptors文件夹中
  • [zqchen@DDB D3Pockets_Descriptors]$ python ./d3pockets_desciptors_rec.py -r fixed.pdb
蛋白质pdb文件与生成的口袋atm/pit文件在同一文件夹
在该文件夹中会生成result_descriptors.txt文件

Druggability

在D3Pockets_Druggability文件夹中
  • [zqchen@DDB D3Pockets_Druggability]$ python27ana ./RandomForest_predict.py ../pdb/HCoV_229E/S_protein/result_descriptors.txt
result_descriptors.txt作为输入，在该文件夹中生成desc2druggabilit.txt