Fig. 3
From: Labeled dataset of X-ray protein ligand images in 3D point cloud and validated deep learning models
Example of a ligand’s 3D point cloud labeling for five different representation types. Two ligands are used for illustration: 4ZV (PDB entry 5cc6, resolution 2.1 Å) and FUL (PDB entry 4z4t, resolution 1.8 Å). Their blobs from their Fo-Fc maps are shown in the top of the panel with a contour of 3σ (image created with Coot). The LigPCDS visualization script was used to draw the ligands’ 3D point clouds. For ligand FUL, it is possible to see the pattern of a ring in the qRank0.95 representation; it results from the cyclic substructure of size six, present in its structure. In ligand 4ZV this pattern is not clear, possibly due to the mobility of this molecule - which is indicated by the presence of noise around its image (blob) and its representations (bottom left and top right of the ligand region – black points labeled as background). Furthermore, the qRank0.95 representation of ligand 4ZV is partially fragmented, with missing points, while for ligand FUL all points with labels are completely covered. There is more visual correspondence between the ligand’s image in the 3σ Fo-Fc maps and the qRank0.95 point cloud.
