MD simulation data: Cryo-EM structures of HCV E2 glycoprotein bound to neutralizing and non-neutralizing antibodies determined using bivalent Fabs as fiducial markers

Associated MD simulation data of various unbound E2 models as described in Cryo-EM structures of HCV E2 glycoprotein bound to neutralizing and non-neutralizing antibodies determined using bivalent Fabs as fiducial markers Contents The four included tarballs contain MD simulation data for the wildtype (8thz_WT_MD) model as well as the HVR1-removed (8thz_dHVR1_MD), N1/N4/N6 glycan-removed (8thz_dN146_MD), and I568V/Q546L/T563V (8thz_I568V/Q546L/T563V_MD) variants. These tar balls contain six folders, Rep_1 to Rep_6, that contain production and data files for each of the six replicas and a toppar folder that contains the topology files used for each simulation. Each replica folder includes: The source .pdb file The .psf file used as input for the simulation Seperate .inp files for equilibration and production that were passed in as input during NAMD execution .xsc and .xst files describing extended system configuration and system cell configuration information for both equilibration and production runs The equilibration trajectory in .dcd format Rep_1, Rep_2, and Rep_3 contain the full production trajectories in .dcd format. Due to upload storage limitations, final production files are omitted for replicas Rep_4, Rep_5, and Rep_6 of each system run. All files to recreate each production run are included for each replica and final trajectory files of Rep_4, Rep_5, and Rep_6 can be provided upon request.