Table 1.

The performance comparison of CSAlign and Flexi-LS-align on a self-alignment benchmark set of 477 compounds in terms of the success rates (percentages of the cases in which RMSD of the highest-score alignment < 2 Å and < 2.5 Å) and the average RMSD of the best-scoring alignments.

Alignment method	Success rate <2 Å (%)	Success rate <2.5 Å (%)	Average RMSD (Å)
CSAlign	96	99	0.61
Flexi-LS-align	73	80	1.67
Flexi-LS-align (option)	77	83	1.47