3.6. Molecular dynamics simulations
The molecular dynamic method is frequently used to analyze atom behavior, structural stability, and atomic-level conformational changes. Molecular dynamic simulations are the most prominent tool used in the all-atom modeling of biomolecules to get insight into the system’s dynamical characteristics. Through MD simulations, the protein interactions, conformational, and structural modification in the protein, and the ligand associated movements within the hydrated environment can be studied.The MD simulation of 200 nanoseconds (ns) was carried out for each complex to measure the behavior of docked complexes in real-time. The MD simulation trajectories were evaluated by the time series of root mean square deviation (RMSD) and root mean square fluctuation (RMSF). Upon ligand binding, the protein in all PPAR complexes does not undergo significant structural changes. However, it is generally known that PPAR has a significant degree of flexibility, particularly in the Ω-loop. This loop is highly disordered and has high molecular flexibility, due to which it remains unmodeled in many PPAR X-ray crystal structures [