Drawing the PDB: Protein-Ligand Complexes in Two Dimensions

The two-dimensional representation of molecules is a popular communication medium in chemistry and the associated scientific fields. Computational methods for drawing small molecules with and without manual investigation are well-established and widely spread in terms of numerous software tools. Concerning the planar depiction of molecular complexes, there is considerably less choice. We developed the software PoseView, which automatically generates two-dimensional diagrams of macromolecular complexes, showing the ligand, the interactions, and the interacting residues. All depicted molecules are drawn on an atomic level as structure diagrams; thus, the output plots are clearly structured and easily readable for the scientist. We tested the performance of PoseView in a large-scale application on nearly all druglike complexes of the PDB (approximately 200000 complexes); for more than 92% of the complexes considered for drawing, a layout could be computed. In the following, we will present the results of this application study.