Figure 1.

Fragment interaction model (FIM). Each element in the target dictionary is a trimer cluster, and trimers belonging to the same cluster share similar chemical properties; Each element in the ligand dictionary is a chemical substructure. The binding sites of the targets are represented by fragments (trimer clusters) information and the ligands are encoded with substructures (fragments) information. We assume that the (binding site) fragment-(ligand) fragment interactions facilitate the site-ligand binding. The interaction between a binding site fragment and a ligand substructure is determined by their distance.