Preparation: Both the ligand and the target molecule are prepared by optimizing their geometries and protonation states. Docking Algorithm: Various algorithms are used to predict the best fit between the ligand and the target. These algorithms consider both the shape and the electrostatic properties of the molecules. Scoring Function: After docking, a scoring function evaluates the binding affinity of the ligand-target complex. This score helps in ranking the different possible conformations.
