Figure 4 | Scientific Reports

Figure 4

From: In silico structural elucidation of RNA-dependent RNA polymerase towards the identification of potential Crimean-Congo Hemorrhagic Fever Virus inhibitors

Figure 4

Post-Molecular dynamics (MD) analysis of CCHFV-RdRp complexes. (A) MD simulated conformations of cmd1, cmd2, cmd3, and two reference compounds, RTP and 2′FdC in the sticks, inside the predicted binding pocket of CCHFV-RdRp. The arrangement of motifs and colors are same as in Fig. 3A. (B) Root Mean Square Deviation (RMSD) of CCHFV-RdRp complexed with presented compounds with distinctive colors are highlighted over a period of 10 ns simulations, while, Root Mean Square Fluctuation (RMSF) of all residues during MD simulation are highlighted below. (C) 2D interaction plot is interactively displayed for all presented compounds complexed with RdRp. (D) Per-residue decomposition analysis for all 5 compounds performed with Amber 16 is presented in a bar chart for highly contributing residues of the predicted binding site of CCHFV-RdRp. (E) H-bond occupancy of particular amino acids in frames throughout 10 ns is displayed for cmd1/2 and 3.

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