Designing coarse grained-and atom based-potentials for protein-protein docking

BMC Structural Biology

Table 1 The designation of the 18 atom types ¹

Atom type	Amino acid	Atom³	Atom type	Amino acid	Atom	Atom type	Amino acid	Atom
N	BKBN²	N		Glu	CD		Leu	CG
Cα	BKBN	CA		Glu	OE1		Lys	CG
C	BKBN	C		Glu	OE2		Met	CG
O	BKBN	O	RNη	Arg	CZ		Met	SD
GCα	Gly	CA		Arg	NH1		Phe	CG
Cβ	Ala	CB		Arg	NH2		Phe	CD1
	Arg	CB	NNδ	Asn	CG		Phe	CD2
	Asn	CB		Asn	OD1		Phe	CE1
	Asp	CB		Asn	ND2		Phe	CE2
	Cys	CB		Gln	CD		Phe	CZ
	Gln	CB		Gln	OE1		Thr	CG2
	Glu	CB		Gln	NE2		Trp	CG
	His	CB	RNε	Arg	CD		Trp	CD1
	Ile	CB		Arg	NE		Trp	CD2
	Leu	CB	SOγ	Ser	CB		Trp	CE2
	Lys	CB		Ser	OG		Trp	CE3
	Met	CB		Thr	OG1		Trp	CZ2
	Phe	CB		Tyr	OH		Trp	CZ3
	Pro	CB	HNε	His	CG		Trp	CH2
	Pro	CG		His	ND1		Tyr	CG
	Pro	CD		His	CD2		Tyr	CD1
	Thr	CB		His	CE1		Tyr	CD2
	Trp	CB		His	NE2	LCδ	Ile	CG2
	Tyr	CB		Trp	NE1		Ile	CD
	Val	CB	YCξ	Tyr	CE1		Leu	CD1
KNξ	Lys	CE		Tyr	CE2		Leu	CD2
	Lys	NZ		Tyr	CZ		Met	CE
KCδ	Lys	CD	FCξ	Arg	CG		Val	CG1
DOδ	Asp	CG		Gln	CG		Val	CG2
	Asp	OD1		Glu	CG	CSγ	Cys	SG
	Asp	OD2		Ile	CG1

ISSN: 1472-6807