Table 3.

Run times of MASS on large-scale protein ensembles

Ensemble name	No. of mol.	Avg. mol. size	Avg. no. of SSEs	SCOP classification	Run time (h:mm:ss)
TIM barrels	62	391	14	same domain	00:47:59
Microbial ribonucleases	63	103	3	same domain	00:00:28
Subtilisin	60	273	14	same domain	00:23:10
Unrelated proteins	60	297	14	unrelated	00:09:42

The performance of MASS as a function of: (1) the number of molecules; (2) the average molecular size; (3) the average number of SSEs in a molecule; and (4) the structural similarity among the molecules. All four parameters increase the running time as they grow.