Selective prediction of interaction sites in protein structures with THEMATICS

BMC Bioinformatics

Table 6 THEMATICS predicted binding clusters for apo and holo structures.

Protein	Ligand	Apo Holo PDB ID	THEMATICS Result
ATP:corrinoid adenosyltransferase	ATP	1G5R	K41	D127	E128	Y131	R161
		1G5T	K41	D127	E128	Y131
Intestinal Fatty Acid Binding Protein	MYR	1IFB	Y14	D34		Y70	R106	Y117	R126
		1ICM	Y14	D34	R56	Y70	R106	Y117
HPV11 regulatory protein	ALQ, 434	1R6K	H29	H32
		1R6N	H29	H32
Proline 3-hydroxylase	FE (II), sulfate	1E5R	R97	H107	H135	H158	R168	H238	Y239	H244
		1E5S	R97	H107	H135	H158		H238	Y239	H244
Glyoxalase 1	Ni(II)	1FA8	H5	E56	Y72	H74	D115	D117		E122
		1F9Z	H5	E56	Y72	H74	D115		Y119	E122
β-Amylase	maltose	1B90	Y14	Y44	D49	H89	Y164	E172	R174			Y310	E367
		1B9Z	Y14	Y44	D49	H89	Y164	E172	R174	Y178	K287	Y310	E367
GlcAT-P	UDP, Mn(II)	1V82	E101	R104	D195	D196	D197	Y200	D254
		1V83	E101	R104	D195	D196	D197	Y200	D254
Retinol-binding protein II	retinal	1OPA	Y19	Y60	C95		C121
		1OPB	Y19		C95	R104	C121

For each protein, the predicted binding cluster for the apo form is given in the top row and for the holo form in the second row. Predictions obtained using a Z score cut-off of 1.0. Residues that make contact with the ligand are shown in bold.

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