Table 2. S calculated with and without P_b for thirty superfamilies using residue pairwise 3D distances ≤ 5 Å and a minimum of 5 intervening residues.

Query	Resolution	Query	Description	Number of	S a				S without Pb
	(Å)	length		sequences	CCM	EVC	GSF	PCVb	CCM	EVC	GSF	PCV
1ayaA	2.05	101	tyrosine phosphatase SH2 domain	12,208	55	54	60	43	56	55	62	44
1b5oA	2.20	382	aspartate aminotransferase	105,741	862	810	774	606	860	805	768	601
1el3A	1.70	315	aldose reductase	67,824	612	588	514	502	607	582	509	499
1k30A	1.90	234	glycerol-3-phosphate acyltransferase	12,225	110	114	90	77	110	112	90	78
1b23P	2.60	184	elongation factor Tu	78,839	167	135	109	101	167	134	109	102
1olzA	2.0	481	Sema4D	5,453	187	245	185	92	184	240	183	91
1wznA	1.90	155	SAM-dependent methyltransferase	146,217	169	156	159	154	164	152	155	149
1z0kC	1.92	164	Rab4 GTPase	64,211	212	181	202	178	209	180	201	175
1zp9A	2.00	258	Rio1 serine kinase	24,076	105	110	91	86	106	111	92	87
2b61A	1.65	357	homoserine transacetylase	47,508	294	290	284	274	294	290	284	275
3ex7H	2.30	241	DEAD-box ATPase eIF4AIII	98,478	254	239	173	157	251	237	173	156
4ag9A	1.76	165	glucosamine-6-phosphate acetylase	107,738	167	174	173	163	164	171	170	163
5dfiA	1.63	318	apurinic-apyrimidinic endonuclease	36,297	293	317	244	193	291	313	242	193
5hf7A	1.54	227	thymine DNA glycosylase	7,588	125	126	72	66	126	125	73	66
5m4pA	2.30	164	pyruvate dehydrogenase kinase	1,651	33	34	37	23	34	36	38	24
1ijxA	1.90	127	cysteine-rich domain of sFRP-3	3,224	24	25	19	20	25	25	20	21
2nrlA	0.91	147	myoglobin	9,514	98	95	68	58	97	94	69	58
4cmlA	2.30	313	INPP5B	4,724	244	247	266	177	242	242	264	176
1jw9B	1.70	249	molybdopterin synthase MoeB	23,170	331	318	272	243	325	312	269	242
3fhkF	2.30	147	disulfide isomerase	1,042	61	64	67	49	61	64	68	49
3h7uA	1.25	335	plant stress-response enzyme Akr4c9	67,652	589	573	502	481	577	565	494	473
1g9rA	2.00	311	galactosyltransferase LgtC	10,575	283	264	281	212	275	254	274	208
4em8A	1.95	148	ribose 5-phosphate isomerase B	7,217	184	181	160	146	173	175	153	138
1i6mA	1.72	328	tryptophanyl-tRNA synthetase	20,731	321	312	198	166	316	309	194	165
3f1lA	0.95	252	oxidoreductase, Ycik	99,991	454	448	433	397	446	439	426	393
1jr3A	2.2	373	bacterial DNA clamp loader γ subunit	24,739	377	373	258	245	373	365	258	245
1nnlA	1.53	225	human phosphoserine phosphatase	130,332	136	133	111	91	137	131	111	93
1frwA	1.75	194	E. coli MobA	79,445	193	179	213	168	194	180	212	169
1bqbA	1.72	301	Aureolysin metalloproteinase	5,289	333	336	254	190	325	331	252	190
2ovdA	1.8	182	human complement protein C8γ	6,874	62	75	53	42	63	75	53	41
				average:	245	240	211	180	242	237	209	179

For each query the optimal S among competing methods is shown in bold. Shaded scores indicate the query for which the optimal method changes when P_b is excluded.

^aHydrogen atoms were added using the Reduce program [21], except for 3f1lA for which hydrogens were already present in the pdb coordinate file.

^bPSICOV version 2.4 using the recommended –p and –d 0.03 options.