4.14.3. Receptor Grid Generation

Receptor grid generation forms the first step of molecular docking protocol. A volume of the active site is represented by the generated grid file. The ligands of interest are then docked in this grid. Initially, the minimized protein was selected to generate the grid. It has been reported in the literature that Argpyrimidine binds to the upstream C-Domain Type 1 in RAGE [69]. Hence, the amino acids from 123 to 219, which represent the upstream C-Domain Type 1, were selected for generating the grid for docking SM and Argpyrimidine. The centroid was generated around these amino acids, and further criteria were set to default, to generate the grid for docking [80,81,82].