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The ranking of the sampled peptide binding modes for both the bound docking cases (bpro-upep) and the unbound docking cases (upro-upep) in PepPro based on the evaluation metrics cL-RMSD (A) and DockQ Score (B). Subpanels show ranking performances using different thresholds of cL-RMSD (2.0 Å, 4.0 Å, and 6.0 Å) and DockQ Scores (0.9, 0.7, and 0.4). Numbers (%) reported in the figures are ranking success rates when top 10, 100, or 1000 models were considered for each prediction.
