I would like to dock simultaneously, three ligands with three different binding sites in the same pentameric protein. Can you please suggest me any ideas and softwars?
Hi Djebaili,
You can do focalized docking using Autodock software by setting the grid around the active site of each ligand. It would be three calculations, one for each ligand.
Hi Martiniano Bello ,
thank you .. yes, I tried to do it but the problem that the autodock parameterizes one grid box on one active site. and I need to parametric three grid boxes around the three different active sites at the same time !!! then lunch the docking for the three ligands in one calculation. Please tell me is it possible !!!
Hi Djebaili,
It is not possible to do it simultaneously with Autodock, only through three calculations as mentioned. You can also explore blind docking with Swissdock although there would also be three calculations.
Is there any rationale to dock to all three sites simultaneously, in the same calculation? I can't see any. Running three separate docking must yield exactly same result.
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