Table 1.

Spearman correlations between the similarity/distance predictions of the listed methods and TM scores.^a

	TMmin			TMmax
	ProstT5	ProtT5	ESM-1b	ProstT5	ProtT5	ESM-1b
EBA	0.92	0.90	0.87	0.86	0.84	0.80
EBAplain	0.56	0.72	0.64	0.20	0.54	0.52
TM-vec		0.81			0.82
pLM-BLAST		0.58			0.60
AD	−0.65	−0.46	−0.46	−0.49	−0.39	−0.39
ProtTucker		−0.46			−0.38
HH-align	0.82			0.77
Needleman–Wunsh	0.61			0.43

^aWhere possible, we showcase the methods performances for ProstT5, ProtT5 and ESM-1b. The EBA scores are normalized according to the TM scores, we therefore compare EBA_min with TM_min and EBA_max with TM_max. Since the other methods provide only one score, the same prediction is compared to both TM_min and TM_max. The expected correlation for similarity scores is positive, while for distances is negative. Best correlation values for TM_min/max in bold.