Table 1.

Comparison of DaliLite v.3, the SSM server and SCOP

Query	Dali −q time (min)	Dali −q P	Dali −q Z AUC	Dali −l time (min)	Dali −l Z AUC	SSM Q AUC	SCOP T	SCOP class
1c52	14	241	0.885	297	0.822	0.674	219	a.3.1.
1sfxA	12	401	0.757	357	0.733	0.386	331	a.4.5.
1azu	14	529	0.967	369	0.969	0.516	289	b.6.1.
1wk2A	7	49	0.800	201	0.966	0.197	60	b.122.1
3be7A	51	542	0.990	1861	0.968	0.843	135	c.1.9.
1qlwA	30	414	0.908	1211	0.897	0.576	456	c.69.1.
2baa	18	726	0.693	486	0.354	0.025	979	d.2.1
1wotA	13	500	0.558	251	0.642	0.009	179	d.218.1

AUC, area under the curve of reliability (TP/P) versus coverage (TP/T), where Ts (‘true’) are members of the same SCOP (Murzin et al.1995) superfamily as the query structure, Ps (‘positive’) are the top n matches from the ranked list for varying n and TPs (‘true positive’) are the intersection of sets T and P. Only PDB entries classified in SCOP v.1.73 were evaluated and each PDB entry was counted once. SSM server http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver; (Krissinel and Henrick, 2004) parameters were set to 10 : 10 and highest precision. The DaliLite search was performed using the –list (Dali –l) or –quick option (Dali –q with MAX_HITS=1000) and reporting matches with Z>2.