I have docked protein BSA with glucose in order to glycate it now i want to dock this complex with a ligand , how am i supposed to do this ?
Any suggestions would be appreciated.
Use Autodock and set the grid to the whole protein. And then perform docking. If possible remove the first ligand and again follow the same. Check whether the ligand bounds to the same region/active site or not. If yes, then search for the allosteric sites and set the grid there. Active sites can be obtained through CASTp or MOLE.
Hi Geethanjali Anilkumar,
if i understand well you want to glycosylate you protein and then perform docking calculation. If this is the case, you should first predict the glycosylation sites and then contruct them. Secondly, this glycosilated protein could be used to perform docking studies. Based on the previusly mentioned, I suggest you to use the following tool to build the gycosilated system, and the docking calculation can be performed as suggested by Pritam with Autodock, by the way you can use swissdock that also provide good docking results.
http://www.charmm-gui.org/?doc=input/glycan
http://www.swissdock.ch/
Hi Geethanjali,
Online molecular docking tools may help you solve this problem, such as AutoDock and RosettaDock. Creative biostructure provides protein-ligand docking and analysis services, I think it’s good, you can try.
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