Molecular dynamics simulation of histone deacetylase enzyme with zinc ion and application

This study aims to generate the system of histone deacetylase enzymes (HDAC) with its cofactor zinc ion using two different parameter models and application of molecular dynamic (MD) study for structure of HDAC2 and vorinostat ligand. Materials and methods: Two non-bonded models, including 12-6-4 Lennard-Jones and cationic dummy atom, were applied for building a solvation system of HDAC2 crystal structure with presence of suber-anilohydroxamic acid (SAHA) and zinc ion.