Example 1: R1-R8 matched to several known 3D structures

• Ligand-complex structures from PDB (Protein Data Bank)
• Ligand 3D structures displayed in black
• The subsequences in R1-R8 were matched to the determined part of 3D structures. (The colors corresnpond to those in G1-G7)

PDB ID (description)	1ZKY (Estrogen receptor)	1DB1 (Vitamin D nuclear receptor)	1RDT (Retinoic acid receptor RXR-α)
Ligand-protein complex
Nearest DrugBank pair (group)	136 <--> DB00957 (R1)	856 <--> DB00136 (R2)	459 <--> DB00523 (R3)
Tanimoto coefficient	0.945	1.0	0.886
PDB ID (description)	2RH1 (β-2-adrenergic receptor)	2RH1 (C8 only)	1BGQ (Heat shock protein 90)
Ligand-protein complex
Nearest DrugBank pair (group)	766 <--> DB00521 (R3)		3279 <--> DB03758 (R4)
Tanimoto coefficient	0.903		1.0
PDB ID (description)	1PGP (6-Phosphogluconate dehydrogenase)	1MAI (Phospholipase C δ-1)	1CZM (Carbonic anhydrase I)
Ligand-protein complex
Nearest DrugBank pair (group)	2678 <--> DB02076 (R5)	3128 <--> DB03401 (R6)	295 <--> DB00311 (R7)
Tanimoto coefficient	1.0	1.0	0.78
PDB ID (description)	1GWV (N-acetyllactosaminide α-1,3-galactosyltransferase)
Ligand-protein complex
Nearest DrugBank pair (group)	3499 <--> DB02379 (R8)
Tanimoto coefficient	1.0