I know the binding sites in both monomers, do I have to preserve the attachment of the ligand to these binding sites, to get binding energy?
User asked 7 years ago
Since I know the binding sites in both monomers, so while doing docking do I necessarily need to mimic (preserve) the attachment of the ligand to these binding sites, so as to get the binding energy?
1 Answers
Dr. Muniba Faiza Staff answered 7 years ago
Yes, since you are well aware of the binding/catalytic sites of the ligand in the protein, therefore, you will have to bind in the specific site, unless you are doing blind docking or trying to find the interactions of the ligand within the protein. Also, make sure that before docking you have removed the already bound ligand from the protein.
