Table 3.

Difficult structure pairs with good alignments found just by one method

Categorya	Total	SSAP	STRUCTAL	DALI	LSQMAN	CE	SSM
All α–All α (same CAT)b	369(8)	0	103 (5)	2 (0)	212 (2)	0	52 (1)
All α–All β	61	0	57	0	2	0	2
All α–Mixed α/β	610	0	275	0	243	0	92
All α–Few Secondary Structure	13	0	7	1	4	0	1
All β–All β (same CAT)b	37 (5)	1 (0)	24 (4)	1 (0)	10 (1)	0	1 (0)
All β–Mixed α/β	318	0	260	1	39	0	18
All β–Few Secondary Structure	0	0	0	0	0	0	0
Mixed α/β–Mixed α/β (same CAT)b	292 (8)	0	130 (4)	1 (0)	111 (1)	0	50 (3)
Mixed α/β–Few Secondary Structure	4	0	2	0	2	0	0
Few Secondary Structure–Few Secondary Structure	0	0	0	0	0	0	0
Total	1704	1	858	6	623	0	216

Good alignments are defined as those where one of the methods finds a good alignment (SAS<4 Å and matches more than 35 residues), while all other methods find bad alignments (SAS>6 Å for any length of match). We also tested other definitions of difficult alignments (e.g. longer matches, or less stringent SAS values) and found a similar distribution amongst the different methods (data not shown).

^aWe categorize the pairs of aligned structures by their class (C) classifier.

^bWe list in parenthesis the number of difficult alignments found with structures of the same CAT classification.