I want to study the interaction of the enzyme with its substrate - glycated protein. I know that the enzyme specifically binds the sugar residue of the protein-substrate. I understand, how to perform protein-protein docking or protein-small ligand docking. But I wonder what approach should I use in my case. What docking software can handle glycated proteins?
I would be grateful for any suggestions.
You can try FTDock (http://www.sbg.bio.ic.ac.uk/docking/ftdock.html) + MultDock, which allows to dock two systems made of any residues / atoms. It's obviously pretty simplified, since it only takes care of shape (through van der Waals interactons) and electrostatics matching, but was shown to give reasonably good results for biological systems.
I have done a protein-ligand docking with AutoDock. The protein contains two glycan chains. My ligands was likely to interact with glycan residues rather than amino acids.
Hi, maybe that question is the one I am asking right now, maybe you have got the answer. But I also tried docking the protein that I had glycosylated and Cluspro is not the best choice because the algorithm doesn't read the glyphs I add to the protein surface. I hope there are other server options
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