Tanshinone IIA/20 bound to NQO1

All docking calculations were performed with the AutoDock Vina program. The crystal structures of human NAD(P)H Quinone Oxidoreductase 1 (NQO1) was used as starting point. The PDB structures of 2F1O was used for the simulations of NQO1. All Molecular dynamics simulations (MD) simulations were performed with the pmemd module of Amber 18 software suite. Molecular mechanics generalized born surface area (MM/GBSA) was performed with mmpbsa.py program, enclosed in Amber 18 software, to estimate the binding free energy. The translational and rotational entropy was calculated with stardard statistical mechanics formulas. The vibrational entropy was computed from the frequencies of global motions by using normal mode analysis (N-mode) in mmpbsa.py program. The coordinates for these calculations are taken from the MD simulations trajectory.All docking calculations were performed with the AutoDock Vina program. The crystal structures of human NAD(P)H Quinone Oxidoreductase 1 (NQO1) was used as starting point. The PDB structures of 2F1O was used for the simulations of NQO1. All Molecular dynamics simulations (MD) simulations were performed with the pmemd module of Amber 18 software suite. Molecular mechanics generalized born surface area (MM/GBSA) was performed with mmpbsa.py program, enclosed in Amber 18 software, to estimate the binding free energy. The translational and rotational entropy was calculated with stardard statistical mechanics formulas. The vibrational entropy was computed from the frequencies of global motions by using normal mode analysis (N-mode) in mmpbsa.py program. The coordinates for these calculations are taken from the MD simulations trajectory.