Large scale MD simulation of 8-oxoguanine and AP site multiple lesioned DNA molecule combined with biomolecular visualization software

Fujimoto, Hirofumi; Pinak, M.; Nemoto, Toshiyuki*; Sakamoto, Kiyotaka*; Yamada, Kazuyuki*; Hoshi, Yoshiyuki*; Kume, Etsuo 

We developed the novel system, Fujitsu Bio Molecular Visualization System (F-BMVS), that enables to produce real pictures and an animation by arranging them along a time series of a large scale simulation of biomolecules associated with a molecular dynamics (MD) simulation program. This animation system is used to study the results of molecular dynamics code, AMBER, in order to find structural differences on the lesioned DNA comparing with non-damaged DNA. These structural differences would be a factor that guides a repair enzyme to discriminate a lesion from non-damaged DNA region.