Figure 1
From: Fast automated placement of polar hydrogen atoms in protein-ligand complexes
A network from PDB structure 1x8x. This figure illustrates the algorithm that is used for optimization. The amine and the hydroxyl group of the ligand are included in the optimization. (a) A 2d-representation of the protein-ligand interface. (b) The graph representation of the hydrogen bond network. (c) Graph after reduction to a tree. The most central node is the root. (d) A depth-first traversal of the tree determines the order in which the nodes are evaluated. The numbers indicate the sequence of score calculation.