Table 1.

3D-BLAST performance with different thresholds of the E-value on structural database searches and automatic SCOP superfamily assignment on the protein query set SCOP-894

Threshold of E-value	Structural database search			Superfamily assignmenta
	Recall	Precision	False positive rate	894 proteins		Sequence identity <25%b
				Correct assignment (%)	Coveragec(%)	Correct assignment (%)	Coverage (%)
e−10	0.60	0.52	0.0091	96.68	97.76	86.32	92.58
e−15	0.50	0.81	0.0020	98.53	91.61	92.77	72.49
e−20	0.43	0.91	0.00056	99.60	84.23	97.60	54.59
e−25	0.39	0.95	0.00016	99.86	77.96	98.94	41.05

SCOP-894 consists of 894 query proteins from two subsets, SCOP95-1.67 and SCOP95-1.69. SCOP95-1.67 has 378 query proteins, which are in SCOP 1.67 but not in SCOP 1.65, and the search database is SCOP 1.65. SCOP95-1.69 consists of 516 query proteins, which are in SCOP1.69 but not in SCOP1.67, and the search database is SCOP1.69.

^aThe first rank in the hit list of a query protein is assigned as the superfamily.

^bThe predicted accuracy was calculated from 229 query proteins having <25% sequence identity.

^cThe coverage is defined as P/T where P is the number of the assigned structures and T is total number of structures. For example, P is 819 and T is 894, and the coverage is 91.61% if the E-value is set to e⁻¹⁵ for the query set SCOP-894.