After Protein-ligand docking Using Autodock Vina, How can I check the structural change in the protein backbone and the ligand?

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Rudy J Richardson

There should be no change in the protein backbone after docking with Vina. However, if you have specified certain residues to be flexible, there may be changes in conformations of residue side chains. If the ligand was set to be flexible, then there would be some change in the ligand conformation after docking -- this could be detected by computing the RMSD for the ligand before and after docking.

Anu Manhas

In addition to Rudy J RIchardson, structural changes can be detected by performing molecular dynamic simulations.

Manne Munikumar

The protein and ligand structural changes can be detected by performing the molecular dynamic simulations.