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

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• 4 configurations
• 1 pipeline
• 1 task
• 3 protocols
• 4 datasets
• 12 evaluations
• 45 results
• 6 evidence claims

Results

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Claims

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• CLAPE-SMB with ESM-2: description: Description Predicts small-molecule-binding residues from sequence alone, using frozen esm2_t33_650M_UR50D residue embeddings with a contrastive-learning binding-site predictor. (Reviewed profile (2026-09-16): summary at Conclusion (paragraph 1); Results/Comparison of CLAPE-SMB with DeepProSite and heuristic analyses in three protein case studies (paragraph 3); architecture fact at Methods/Sequence embedding (paragraph 2); Methods/Loss function (paragraph 5); description text also read at Abstract)
• CLAPE-SMB with ESM-2: uses model ESM-2: Uses model ESM-2 (Methods: esm2_t33_650M_UR50D frozen embeddings followed by 5-layer MLP)
• COACH420, trained on CHEN11 (protein-small molecule binding-site prediction): links:evaluates_task:reported-task-b181ed450cdd41: Evaluates task protein-small molecule binding-site prediction (Comparison of CLAPE-SMB with other models trained on CHEN11 and tested on COACH420; Table 2 (Tab2), row 2 P2Rank, column 2: COACH420, trained on CHEN11 Recall; Table 2 (Tab2), row 3 GraphBind, column 2: COACH420, trained on CHEN11 Recall; Table 2 (Tab2), row 4 CLAPE-SMB, column 2: COACH420, trained on CHEN11 Recall)
• Reported AUROC for CLAPE-SMB with ESM-2: Printed value 0.917 (Table 5, ESM-2 / SJC row, AUROC column)
• SJC test split (protein-small molecule binding-site prediction): links:evaluates_task:reported-task-b181ed450cdd41: Evaluates task protein-small molecule binding-site prediction (Comparison of CLAPE-SMB with other models on the SJC; Table 3 (Tab3), row 2 P2Rank, column 2: SJC test split Recall; Table 3 (Tab3), row 3 GraphBind, column 2: SJC test split Recall; Table 3 (Tab3), row 4 DeepProSite, column 2: SJC test split Recall; Table 3 (Tab3), row 5 CLAPE-SMB, column 2: SJC test split Recall)
• UniProtSMB test split (protein-small molecule binding-site prediction): links:evaluates_task:reported-task-b181ed450cdd41: Evaluates task protein-small molecule binding-site prediction (Comparison of CLAPE-SMB with other models on the UniProtSMB; Table 4 (Tab4), row 2 P2Rank, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 3 GraphBind, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 4 DeepProSite, column 2: UniProtSMB test split Recall; Table 4 (Tab4), row 5 CLAPE-SMB, column 2: UniProtSMB test split Recall)

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