Table 4.

The effectiveness of the suboptimal alignment search by hybrid method

		Average Improvement
Benchmark subset	% Alignments improved	RMSD (Å)	CMO (%)
High similarity	34	6.2 (1.5) to 4.8 (1.4)	52 (6) to 56 (7)
Moderate similarity	48	9.1 (2.3) to 6.5 (1.7)	36 (8) to 40 (4)
Low similarity	65	12.3 (1.9) to 8.7 (1.9)	26 (9) to 33 (5)
Undetectable similarity	78	13.7 (2.0) to 9.5 (2.1)	19 (11) to 27 (11)

The average improvement of RMSD and CMO. Values of variance are given in parentheses. (RMSD) Root mean square deviation; (CMO) contact map overlap.