PDB4DNA: Implementation of DNA geometry from the Protein Data Bank (PDB) description for Geant4-DNA Monte-Carlo simulations

Abstract This paper describes PDB4DNA, a new Geant4 user application, based on an independent, cross-platform, free and open source C++ library, so-called PDBlib, which enables use of atomic level description of DNA molecule in Geant4 Monte Carlo particle transport simulations. For the evaluation of direct damage induced on the DNA molecule by ionizing particles, the application makes use of an algorithm able to determine the closest atom in the DNA molecule to energy depositions. Both the PDB4DNA app... Title of program: PDB4DNA Catalogue Id: AEWB_v1_0 Nature of problem To evaluate strand breaks induced on the DNA molecule by ionizing particles using Monte Carlo method. It requires the implementation of DNA geometry, physical processes adapted to nanodosimetry simulations and an algorithm to determine the closest atom in the DNA molecule to energy depositions. Versions of this program held in the CPC repository in Mendeley Data AEWB_v1_0; PDB4DNA; 10.1016/j.cpc.2015.02.026 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)