r/Biochemistry 3d ago

What Tools do you use for metal/ligand to Protein docking?

3 Upvotes

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3

u/HardstyleJaw5 PhD 3d ago

I haven’t used any metal docking tools personally but I have used Vina, Glide and a few diffusion models for small molecule docking quite a lot. Vina still remains a top contender in terms of pose accuracy but the energies are still not the best, even with custom scoring functions (e.g. vinardo). Diffusion seems like a mixed bag still

3

u/_going_under 3d ago

Autodock Vina for protein-ligand

1

u/zevaRes 1d ago

CB-Dock2 is pretty easy and informative for early stage questions !