Model
The affinity of GRIN2B protein and main chemicals in rose flavonoids by molecular docking
In this study, we employed a semi flexible docking method.
Firstly, we downloaded the crystal structure of the target protein GRIN2B from a protein database or modeled it using AlphaFold3. Then, we used Maestro computational software to prepare the structures of proteins and small molecules separately. During the protein preparation process, optimize the hydrogen bond network and minimize the energy of the protein system. Small molecule preparation: Generate three-dimensional structures and minimize energy, and generate multiple conformations (15) to increase the likelihood and accuracy of successful docking. Next, we use the sitemap module of Maestro software to predict the binding pocket of small molecules (default parameters) and generate a receiver grid file. Based on the predicted pocket location, size, and small molecule docking score, we determine the most likely binding pocket. The other parameters remained at their default values. During molecular docking, select the prepared grid file and small molecules in the small molecule docking ligand docking module for molecular docking. Based on the scoring of docking results and the rationality of small molecule binding conformation, the optimal binding mode is selected through comprehensive analysis and judgment. The docking results were visualized using Pymol software.
All molecules were docked using 7KL0 as a template, the molecular binding pockets were predicted,
and the reasonable ones were found. Molecular docking was performed between the compounds and the target protein (GRIN2B), and molecular dynamics studies were conducted. From the RMSD results, it could be seen that after 10 ns, the molecules and protein tend to stabilize, and six main rose flavonoids were proved to tightly combine with GRIN2B protein with different affinities.
