Molecular dynamics simulations of the binding stability of selected terpenes towards NS5B RNA polymerase from hepatitis C virus.

MD simulations examining the stability of terpene-protein complexes. These resutls ahve been published as " Tomasz M. Karpinski, Marcin Ozarowski, Pedro J. Silva , Mark Stasiewicz, Rahat Alam and Abdus Samad (2023) Discovery of terpenes as novel HCV NS5B polymerase inhibitors via molecular docking Pathogens, 12:842 " xxx.zip contains PDB files of every complex throughout the molecular dynamics simulations, taken at 2.5 ns intervals (simulation time). Filenames follow the format xxxx_nnn.pdb , where xxx is the ligand name and nnn is equal to simulation_time (in ns) divided by 0.25. RMSD.zip contains the tables with the RMSD values of protein and ligand upon comparing each complex snapshot with: A) its initial structure (xxx_RMSD_vs_0.tab) B) its structure after 25 ns simulation time (xxx_RMSD_vs_100.tab) C) its structure after 75 ns simulation time (xxx_RMSD_vs_300.tab) D) its structure after 150 ns simulation time (xxx_RMSD_vs_600.tab)