Fig. 6

MDS analysis of protein-ligand complex. 6(A) Simulation results for AKT1_Tadalafil complex and 6(B) Simulation results for MDM2_Finasteride complex. The graphs show (i) PL-RMSD of simulated C-alpha atoms of protein in complex with inhibitor during 100 ns MD simulation. The X-axis shows the variation of protein RMSD through time and the Y-axis shows the variation of protein RMSD through time. (ii) P-%SSE histogram showing protein secondary structure element distribution by residue index throughout the protein structure complexed with the ligand. Red columns indicate the alpha helices and blue columns indicate the beta-strands. (iii) PL-Contacts histogram showing four types of protein interactions (H-bonds, hydrophobic, ionic, and water bridges) with the ligand throughout the simulation. The stacked bar is normalized over the course of the trajectory. (iv) Timeline representation of the interactions and contacts. The top panel shows the total number of specific protein contacts with the ligand and the below panel shows the specific residues which interact with the ligand in each trajectory frame (dense areas represent more than one contact with the ligand). (v) P-RMSF of simulated protein in complex with inhibitor during 100 ns MDS. (vi) Schematic 2D diagram of ligand atom interactions with the protein residues (interactions that occur more than 30% of the simulation time in the selected trajectory from 0 to 100 ns are only shown)