Figure 2
From: Modeling regionalized volumetric differences in protein-ligand binding cavities
Computing fragments. Input cavity A (light blue,A) and B (light red,C). Fragments derived from AB and BA, labeled with lower case letters, original cavities outlined in dotted lines (B). Fragments translated into connected components (solid lines, labeled G 1 -G 4 ), original cavities outlined in dotted lines (D). A ray (arrow) from a corner of G 4 , drawn from the enlarged perspective of the dark box in D (E). The directed graph, H, with nodes G 1 − G 4, connected based on containment. The dotted line separates nodes of different depths. Yellow ovals indicate subgraphs relating to the same fragment, labeled with lower case letters (F). Cavity A is shown atypically, in a disconnected manner, to illustrate the algorithm.