Fig. 4: Prediction results of PMM and other predictors for transition metals.

a Performance comparison of five zinc-binding site predictors (PMM, GRE4Zn, TEMSP, ZincBindDB, CHED). Bar plots represent precision, recall, and F1-score, while the line plot shows the average zinc deviation (Å) for available methods. b Comparison between Metal3D (orange) and PMM (blue) for transition metal binding sites in the test set. c–f Comparison of native and predicted metal binding sites in 2zp9. c Native structure of 2zp9, with five observed zinc sites (Zn1–Zn5, gray spheres). d Predicted metal binding sites by PMM. e Predicted metal binding sites by Metal3D. Both PMM and Metal3D identified the five known zinc sites (pre1-pre5) and predicted three potential sites (pre6-pre8, blue spheres) at their thresholds (PMM: 0.5, Metal3D: 0.75). Metal3D also found three low-confidence sites (pre9-pre11, cyan spheres) with certainty scores above 0.5 but below 0.75. The certainty scores for PMM predictions (pre1-pre8) were 0.94, 0.93, 0.93, 0.92, 0.96, 0.94, 0.94, and 0.93, respectively. The certainty scores for Metal3D predictions (pre1-pre8) were all 1.0, with pre9-pre11 certainty scores of 0.53, 0.50, and 0.51. No statistical hypothesis testing was performed. f AlphaFill Predictor: no metal ions were predicted by AlphaFill. Predicted sites for PMM and Metal3D were obtained at a threshold of 0.5.