PDB ligand extraction and Autodock box creation

I am trying to create a workflow that extracts ligands from a PDB file input and finds their coordinates for alter use in docking through Autodock like software that I plan to integrate into the workflow in Python.

One of the key things to keep in mind is that I want to be able to use .pdb files that are not yet registered in the PDB database itself and so the workflow should run without calling the database for anything (hopefully).

Please find the workflow in it’s current state attached:
consensus_docking2.knwf (71.0 KB)

I start by cleaning the PDB file with the pdbfixer library.

I then use the Biopyhon package to separate all the ligands from the file and output a unique .pdb file for each

However, when I try to read these files back into the workflow, both the PDB loader and Load Local PDB Files nodes seem to be able to read the file but I cannot translate them into SDF or SMILES using OpenBabel or any of the other translators available.

Additionally, I would like to ask if there is way to locate the coordinates of a ligand in a PDB file easily and draw the box surrounding the ligand that is ised by software like Autodock

Thanks in advance!

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Hi @Antoine_Lacour,

sorry for the delayed response. I will have a look at the issue and get back to you soon.

Best regards,

Hi @Antoine_Lacour,

I had a look but I’m not too familiar with some of the extensions you are using.
However, the translation should still work, so I am wondering if it would be possible for you to provide me an example PDB that you were using in the workflow so that I can try it out.
Maybe I can find out why the translation is failing.


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