SILCS (Site Identification by Ligand Competitive Saturation) is a computational method that identifies which functional groups bind on various components of protein surface using MD with multiple small-ligand molecules.
In SICLS, a protein is computationally put into an aqueous solution that contains different types of small molecules. The system containing protein of interest, water molecules and multiple small molecules is subjected to MD simulations for competitive binding. Snapshots taken from these trajectories are combined to generate 3D probability maps - FragMaps. FragMaps demonstrate which types of functional groups bind more strongly on different parts of protein’s surface.
For examples of previously performed studies in which SILCS: Site Identification by Ligand Competitive Saturation was the primary method used, see the following example cases: