Scripts for model refinement of HERVK CA hexamer based on cryoET density map and molecular dynamics simulations of a hexamer-of -hexamers (HOH) assembly. The scripts are separated into folders: 1. RosettaCM_refinement: Contains the input cryoEM density files, pdb strucutres and fasta files for refinement of a HERVK CA hexamer using RosettaCM. Bash scripts to run prepare the structure for refinement and to perform refinement using RosettaCM are included. 2. MD_simulation: Contains the scripts to run minimization, heating, restraint release, tempering, equilibration and production simulations of a HERVK CA HOH assembly. Input structures and forcefield parameters are also included as well as snapshots of initial and final coordinates for 200ns of MD NVT production simulations. The folder subdivided in two for the simulation of the HERVK CA HOH in complex with cofactor IP6 or in its absence.

{"references": ["Krebs, Anna-Sophia, et.al. (2023) MD simulation data associated with \"Molecular architecture and conservation of an immature human endogenous retrovirus\""]}