Table 2.

Comparison of structural alignments quality of similar binding sites on 10 protein pairs with dissimilar folds

First protein structure			Second protein structure			ProBiS	DaliLite	MolLoca	MultiBindb
PDB	Residue numbers	Ligand	PDB	Residue numbers	Ligand	RMSDs (Å)
1addA	262,295,181,15,214,238	ZN	1bmcA	168,90,152,86,88,149	ZN	6.53	14.31	13.29	14.59
1eceA	114,162,238,116,161,27	BGC	2dnjA	212,39,134,252,7,170	DNA	9.91	12.91	12.48	8.05
1phrA	12,129,18,19	SO4	1vhrA	124,92,130,131	EPE	1.50	8.94	8.10	5.37
1bmfA	269,270,273,175,176	ANP	1aylA	268,269,213,254,255	ATP	2.34	n/a	3.26	11.93
1ampA	179,117,256,97,228	ZN	1alkA	51,327,331,370,102	ZN	2.14	10.69	6.60	11.91
1ribA	84,237,238,118,121,122	FEO	1vhhA	130,148,127,135,139,142	ZN	4.82	n/a	n/a	13.19
1powA	308,311,286	FAD	1inpA	311,370,358	n/a	1.07	35.70	19.75	n/a
1alkA	369,327,101,331,370,166	ZN	1fjmA	64,92,208,125,173,221	MN	7.00	n/a	9.63	7.92
1qbaA	844,845,847,850,849,852	n/a	1eurA	176,177,179,182,181,184	n/a	0.27	46.12	0.30	n/a
2kauC	134,136,219,246,320,364	NI	2mhrA	54,25,106,77,73,62	FEO	12.68	25.95	12.41	12.62
	Mean RMSDs (Å)					4.82	22.09	9.54	10.69

^aGeometry+atom type method is used; in the two cases, where ligands are not available (n/a), we restricted the comparison to the corresponding residue numbers given above.

^bThe compared binding sites are defined by the surface region within 8.0 Å from small ligands with codes ZN, MN, SO4, EPE, NI and FEO; the default threshold of 4.0 Å is used elsewhere.