Original Paper\ DiffDock GitHub\ FlowChart_ForToolsUse.pdf
[ ] Obtain LigPlot License
[ ] Install Miniconda
[ ] Open Conda Terminal
[ ] Create folder C:\tmp (Windows) or /tmp (Mac/Linux)\
Linux/Mac Users: Run mkdir /tmp
\
Windows Users: Run mkdir C:\tmp
[ ] Download Chimera
[ ] Download LigPlot
[ ] Open LigPlot (ensure the tmp folder path is set correctly)
[ ] Download 2hyy_single.pdb from this reposistory
[ ] Run git clone https://github.com/tkella47/BioChem_DiffDock.git
to get the pdb and python files you need to download.\
[Requires Git]
Is LigPlot not opening?
[ ] You may need to install Java \ Warning: Mac Users \ There is an x64 Java and ARM64 Java. This relates to the chip on your computer. \ If you have an M1 or M2 chip, ARM is for you. Otherwise, download x64 Java.\ Don't know how to check? Visit
In Chimera(X), open the 2hyy_single.pdb
Then open rank#.sdf
(Sidenote, you can see all the test ligand positions by opening rank#_reversediffusion)\ Take a moment to investigate the beauty that is biochemistry
Under File, Click save. Alternatively Ctrl(Windows/Linux)+S or Command(Mac)+S
Make sure that both the sdf model and pdb model are selected.
Give your file a name and save it.
Next download process_ligand_protein.py
Navigate to the same directory as process_ligand_protein.py. Ensure that process_ligand_protein.py and the pdb from the previous step are in the same folder.
Then run
python process_ligand_protein.py PATH_TO_YOUR_SAVE_FILE.pdb
This will save a file diffdocked.pdb
in the same place as the python file.
If the above code does not work, run the code below. Additionally, if you wish to provide a different name or path for your file simply run.
python process_ligand_protein.py PATH_TO_YOUR_SAVE_FILE.pdb --output_path DESIRED_NAME_OR_PATH/diffdocked.pdb
Open the DiffDocked PDB file first
Make sure LigPlot is open \ Click File: Open : \ Browse : Open diffdocked.pdb
Download 2HYY.pdb\ Click File: Open: \ Browse : Open 2hyy.pdb
In the bottom right hand corner, you can split the screen to see the difference between the docked ligands