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Cofactors

Open twidatalla opened this issue 2 years ago • 2 comments

Hello, an enzyme I am interested in docking has a very important co-factor - NAD, which is included in my PDB crystal structure. Is there any way I can dock molecules to this PDB with the Co-factor included? I tried docking a couple hundred fragments and a lot of them overlap with the NAD so I'm assuming it was just removed from the PDB before docking.

twidatalla avatar May 13 '23 00:05 twidatalla

This would be great -- we're talking about this in the context of an enzyme that binds FAD...

cdsnow avatar May 17 '23 21:05 cdsnow

Hi, unfortunately, the answer is that at the moment DiffDock does not take into account ligands in the input pdb files and therefore cannot consider the effect of cofactors. It could indeed be a very useful addition to the model, but it requires, among other things curating some data for it. At the moment, I don't have the bandwidth for this addition, but hopefully, it will come in the future.

Btw if you are interested in leading the effort on this exciting front, please reach out to me!

Gabriele

gcorso avatar May 18 '23 15:05 gcorso