Table 1. Atom types used in binding site matching.

Atom Type	Atom Subtype	Label
Carbon (C)	Carbonyl C	1
	Aliphatic C, CA, Other sp3 C,	2
	Aromatic C	3
Oxygen (O)	Backbone O and carbonyl O in Asn and Gln, carboxyl O in Asp and Glu	4
	Hydroxyl O in Ser, Thr and Tyr	5
Nitrogen (N)	Backbone N, TRP side chain NE1, GLN NE2, ASN ND2, ARG NE NE1 NE2, LYS NZ	6
	HIS side chain NE1, NE2	7
Hydrogen (H)	polar H	8
Sulfur (S)	Disulfide bond S, Met S, Cys S	2