I have superimposed the structure of an enzyme after ligand (Inhibitor) binding with said enzyme and got RMSD value 0. If any change in the protein structure may occur then how to determine this computationally?
Please help me. Thanks in advance.
In most of the docking algorithms, the proteins are rigid. This is why you have an RMSD value 0. You can perform MD simulations and free energy calculations if it suits your purpose and system.
I supose you mean reversible. It should be irreversible. Irreversible inhibitors do fit better than any inhibitor and no activity is shown. Maybe by this fact. (RMSD 0.no change at all?)
Dear Rahul,
You've got the valid point, and you are not wrong; once you try to dock a ligand and generate a grid around the receptor, your receptor is treated as rigid, and your ligand will dock flexibly. For further studies on atoms behaviour, you can go for MD simulation, which will give you the actual deviation.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Enzymology
- Enzymes