Is there any graph/plot can be generated which signifies the structural change? Is there any way to understand wheather the protein is functional or not? Please suggest.
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.
In addition to Rudy J RIchardson, structural changes can be detected by performing molecular dynamic simulations.
The protein and ligand structural changes can be detected by performing the molecular dynamic simulations.
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