Fig. 4: Mean absolute deviation of correctly predicted sites and selectivity for other ions.
From: Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins
a For all sites where predicted and experimental location are available (true positives in Fig. 3) we compute the mean absolute deviation (MAD) using Metal1D, Metal3D, BioMetAll, MIB and MIB2 on the test set. Some tools predict multiple locations (n) per site (TP). *For MIB and MIB2 we used 2 structures less because the server did not accept these structures. For each tool the whisker plot indicates the median (white dot) and the first quartiles (black box), kernel density estimation of all data points shown as violin plot with minima and maxima indicated by whiskers. b Precision and recall for the test set and 100 randomly drawn structures (except 93 for NI, 68 for CU, 57 for FE2, CO for 30) for other transition (blue), earth-alkali (pink) and alkali (brown) metals. Metal1D as light squares, Metal3D as circles. Threshold used for Metal3D p = 0.75, threshold used for Metal1D t = 0.75.
