TABLE 1.

Clustering algorithms and parameter ranges/values evaluated during optimization.

Algorithm	Parameter	Range/values	Optimal value
Greedy clustering	RMSD threshold	0.5–10 Å	1.25 Å
Agglomerative clustering	RMSD threshold	0.5–10 Å	1.25 Å
	Linkage criterion	Complete, average, and single	Complete
Affinity propagation	Preferences	−5 to 4	Median (RMSD matrix)
DBSCAN	RMSD threshold	0.5–5 Å	1 Å
	Minimum samples	2 and 5	2
OPTICS-xi	RMSD threshold	0.5–5 Å	1.5 Å
	Minimum samples	2	2
	xi	0.005–0.5	≤0.01
OPTICS-DBSCAN	RMSD threshold	0.5–2 Å	1 Å
	Minimum samples	2	2
K-means	Initialization	Random, K-means++	K-means++
Butina clustering	RMSD threshold	0.5–5 Å	1 Å
	Reordering	True and false	False