*3.5. Molecular Dynamic Simulation*

The molecular docking technique is comparatively rapid and imprecise. The docking deficiencies and flexibility of protein may interfere with protein–ligand complex. However, molecular dynamic simulations are computationally expensive and time-consuming but provide reliable and accurate illustration of protein displacement. Considering these facts, molecular dynamic simulations were undertaken using Desmond software package [58,59]. The root-mean-square deviation (RMSD) patterns provide significant insight into average change in displacement of atoms with respect to a frame. The RMSD trajectory provides information about the structural configuration of protein. It is computed for each frame of the trajectory. In order to gain insight into the structure of a protein, it is important to monitor the protein's RMSD. Plotting the RMSD of the ligand is possible once the protein– ligand complex is aligned on a reference protein backbone and the RMSD of the ligand heavy atoms is measured. It is likely that the ligand has diffused from its initial binding site if measured values exceed the protein's RMSD by a substantial margin. Molecular dynamic trajectory analysis is also used to determine the root-mean-square fluctuation of the targeted protein.
