3.5 Molecular docking studies
Molecular docking studies were carried out by AutoDock 4.2 in order to predict the preferred binding state as well as the binding site of the thymol, carvacrol, beta-elemene, trans-caryophyllene, germacrene-D, spathulenol, and 5alpha-pregnane compounds (as well-known allelochemicals of amaranth) with PsbA and PsbS proteins. These compounds are highly bound to these proteins. According to the results (Table 5), the 5alpha-pregnane compound with more negative binding energy as well as its lower inhibition constants compared to other compounds indicates a more stable and better binding to PsbA and PsbS encoded proteins. After the 5alpha-pregnane, the trans-caryophyllene, germacrene-D, spathulenol, beta-elmenene, thymol, and carvacrol compounds were placed in next rank, respectively. The site effect and amino acids involved in the binding of these compounds are shown in Figure 2 to 8.