2.4.5 Binding site prediction (Protein-ligand docking)

The SAMSON software (https://www.samson-connect.net/) was used for binding site prediction. It uses the interaction energy between the protein and a simple Van der Waals probe to locate energetically favorable binding sites. This software uses Auto-docking Vina as an element to maximize the accuracy of these predictions while minimizing the computer time. The program works based on quantum mechanics. It predicts the potential affinity, molecular structure, geometry optimization of the structure, vibration frequencies of coordinates of atoms, bond length, and bond angle. Following the exhaustive search, 100 poses were analyzed and the best scoring poses were used to calculate the binding affinity of the ligands. The ligands that tightly bind to a target protein with a high score were selected. The proteins were docked against the compounds chitosan and cu using SAMSON software (https://www.samson-connect.net/). The 2D interaction was performed to detect the favorable binding geometries of the ligand with the proteins using Discovery studio software to generate the 2D interaction image of the Docked protein-ligand complex with a high score to the predicted active site. The ligands were docked with the target protein and the best docking poses were identified.