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

<p>MD simulations examining the stability of terpene-protein complexes. These resutls ahve been published as   " Tomasz M. Karpinski, Marcin Ozarowski, <strong>Pedro J. Silva</strong> , Mark Stasiewicz, Rahat Alam and Abdus Samad (2023) Discovery of terpenes as novel HCV NS5B polymerase inhibitors via molecular docking    <a href="https://doi.org/10.3390/pathogens12060842" target="_blank"><em>Pathogens</em>, 12:842</a>   "</p> <p><br></p> <p><br></p> <p>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.</p> <p><br></p> <p>RMSD.zip contains the tables with the RMSD values of protein and ligand upon comparing each complex snapshot with:</p> <p>A)  its initial structure (xxx_RMSD_vs_0.tab)</p> <p>B)  its structure after 25 ns simulation time   (xxx_RMSD_vs_100.tab)</p> <p>C)  its structure after 75 ns simulation time   (xxx_RMSD_vs_300.tab)</p> <p>D)  its structure after 150 ns simulation time   (xxx_RMSD_vs_600.tab)</p> <p><br></p> <p><br></p>