2.9 Molecular docking analysis
Molecular docking simulations were performed by Autodock 4.2 (Rashtbari et al., 2017; Yektaet al., 2017). All water molecules were removed by Auto Dock Tools and polar hydrogen atoms, KOLLMAN atoms charge were added to PsbA and PsbS, and docking calculations were performed using Lamarckian genetic algorithm (LGA). The Grid Box was placed at center of PsbA (X center: -8.337, Y center: -50.07, Z center: 38.514) and PsbS (X center: -13.053, Y center: -5.89, Z center: 23.526). The grid map for spacing the midpoints of XXĂ… for PsbA and PsbS were 0.508 and 0.375 angstroms, respectively. The numbers of points in the XYZ dimension were 126*126*126 angstroms, respectively. After docking analysis, the lowest binding energy conformation was selected for each target. The interactions of the PsbA and PsbS protein complexes with thymol, carvacrol, beta-elemene, trans-caryophyllene, germacrene-D, spathulenol, and 5alpha-pregnane compounds were also analyzed using UCSFChimera and Discovery Studio 4.1 Client.