Hello,
We need the pdb of metformin for docking studies in ClusPro.
We tried to make it from the 5G5J pdb but that pdb does not work in ClusPro. I added the pdb we made by splitting from 5G5J. Pymol can recognize it but not ClusPro.
Any recommendation would be helpful.
Thanks,
Bidisha
HI Bidisha Sengupta
You can obtain the 3D structure of Metformin from PubChem (https://pubchem.ncbi.nlm.nih.gov/compound/4091#section=3D-Conformer)
You can convert the sdf file format to pdb either using Avogadro, OpenBabel, or any other relevant software.
Hope this help. All the best
If you mean this ClusPro https://cluspro.org/ that you want to use?
It is said clearly that it is a protein-protein docking server. Metformin is not part of protein structure, it is a small molecule ligand.
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