Figure 1. Knowledge base of protein microenvironments linked to ligand fragments.

For each protein-ligand complex from the PDB, we identify residue atoms interacting with the ligand and note the ligand atoms proximal to them (semi-transparent shaded regions) (top). Next, the FEATURE microenvironments of the residue atoms are calculated (semi-transparent circles) (center). We then map ligand atoms to their pre-computed fragment lists and link them to their proximal microenvironments to form the knowledge base (bottom).