An interaction-motif-based scoring function for protein-ligand docking

BMC Bioinformatics

Table 1 Atom types and descriptions

Atom type	Description	Example^b	On protein	On ligand
C2N	C, SP2, normal/non-polar	-C=C-		x
C2P	C, SP2, polar	-C=O	x	x
C3N	C, SP3, normal/non-polar	-C-C-	x	x
C3P	C, SP3, polar	-C-OH	x	x
CRN	C, aromatic, normal/non-polar	a benzene carbon	x	x
CRP	C, aromatic, polar	a halogenated aromatic carbon	x	x
O2A	O, SP2, hydrogen bond acceptor	>C=O	x	x
O3A	O, SP3, hydrogen bond acceptor	C-O-C		x
O3B	O, SP3, both	-OH	x	x
OLC	O, aliphatic, charged	-COO^-	x
ORA	O, aromatic, hydrogen bond acceptor	oxygen in furan		x
NLA	N, aliphatic, hydrogen bond acceptor	-NR₂	x	x
NLB	N, aliphatic, hydrogen bond donor	-NH_1or2	x	x
NLC	N, aliphatic, charged	-NH₃⁺		x
NRA	N, aromatic, hydrogen bond acceptor	a non-protonated aromatic nitrogen		x
NRD	N, aromatic, hydrogen bond donor	a protonated aromatic nitrogen	x	x
NRE	N, aromatic, either H.B. donor or acceptor	nitrogen (protonated or not) of imidazole	x
S3N	S, SP2, normal/non-polar	-SH	x	x
SRA	S, aromatic, hydrogen bond acceptor	sulfur in an aromatic ring		x
SLC	S, aliphatic, charged	-SO₄^-2		x
PHO	Phosphorus			x
MET	Metal^a		x
HAL	Halogen	F, Cl, Br, I		x

^a Metal ions, such as Zn, were considered in this work as an extended interaction site of the protein molecule.
^b See Fig. S3 in Additional file 1 for a representative chemical structure of the atom type CRN, CRP, ORA, NRA, NRD, NRE, and SRA.

ISSN: 1471-2105