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Docking

Code for Docking

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saveena
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62 views1 page

Docking

Code for Docking

Uploaded by

saveena
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as RTF, PDF, TXT or read online on Scribd
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# Stepwise Docking

A) Ligand Prep :
• SMILE(HMDB0000048) - mol2 .206 using openbabel
• verified non zero
• mol2 to pdbqt -hpc server - file move prepare_ligand4.py - run mol2_pdbqt.py

B ) Receptor Prep
• PDB Downalod 8U1F .206 server
• Rn Grid parameter - paste that line to google sheet and get
• Than PDB to Pdbqt - move prepare_receptor4.py - create vi pdb_pdbqt.py -
python pdb_pdbqt.py

C) GPF _ DPF
move autogrid , move dutodock and gfp.py dfp.py and create code for creation vi
final_gpf_dpf.py
python final_gpf_dpf.py

D) Docking
docking.sh

selected_ChainParameter_file.csv

PDB,Grid spacing,"units(x,y,z)",X center,Y center,Z center


8G7O,0.65,119,223.1805,265.765,195.6535
6E5V,0.5,120,36.748,-65.8645,-9.06
6D67,0.6,115,11.8695,1.1015,-20.4815
7XZ6,0.5,119,115.354,84.696,132.3955
6X5Q,0.5,106,-3.3125,-9.8165,13.7255
6RZ5,0.7,105,7.222,-16.1895,8.498
5JL9,0.5,122,83.746,55.099,48.9855
6TLC,0.8,119,4.454,26.626,55.7035
3GPC,0.6,107,23.811,-13.9265,11.7595

dt['units(x,y,z)']['8G7O']
dt['Grid spacing']['8G7O']
dt['X center']['8G7O']
dt['Y center']['8G7O']
dt['Z center']['8G7O']

import pandas as pd
dt=pd.read_csv('s.csv')
dt.index=dt['PDB']

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