Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning

Table 5 Comparison of prediction accuracy between ProtBert and ESM-2 as the feature extractor of CLAPE-SMB

Feature extractor	Dataset	MCC	AUROC	AUPRC
ProtBert	SJC	0.352	0.856	0.354
ESM-2	SJC	0.535	0.917	0.564
ProtBert	UniProtSMB	0.488	0.922	0.498
ESM-2	UniProtSMB	0.704	0.961	0.750

ISSN: 1758-2946