<b>MD package of wtXPD-damaged-ssDNA</b>

Abstract

MD simulation: wtXPD-damaged-ssDNAXPD-64PP.tgz and XPD-CPD.tgzThe 8 µs MD simulations of human XPD bound to damaged ssDNA, containing a 6−4PP (XPD-64PP) or a CPD (XPD-CPD) lesion right outside the entry pore of XPD, are provided.Descriptions of each simulations1. Simulation of XPD-64PP reveals that 6−4PP initially positioned outside the entry pore is translocated in the 3' to 5' direction as its bases flip into the unoccupied space within the pore.2. Simulation of XPD-CPD reveals that CPD initially positioned outside the DNA entry pore undergoes a backbone-translocation into the pore, but its bases are blocked from entering.Files includedFor each system, the trajectory files are presented in binary NETCDF format, *.nc, a corresponding topology PRMTOP files, *.top, and the coordinates of the initial structure in PDB files, *.pdb are also provided, where * = XPD-64PP, XPD-CPD.Note1. Water molecules and ions are not included in all files.2. The trajectories were saved every 1 ns.</h4