Flat and Easy: 2D Depiction of Protein-Ligand Complexes

Visualization of molecular complexes is commonly used to support the investigation of interaction patterns formed between the members of a molecular complex ensemble. Similar to the representation of single small molecules as structure diagrams, a schematic two-dimensional design of molecular complexes features several advantages. This visualization mode enables the peer to scan large numbers of complexes in short time, originating for example from a virtual screening or de novo design campaign, and to get an impression of their quality. In addition, the diagrams can be printed on hardcopies without information loss and are therefore well suited for publications and talks. We will give an overview of the existing algorithms for the automatic generation of two-dimensional complex diagrams. The reduction of dimensions from three to two is a quite difficult task since the resulting layout has to be more or less free of overlaps and has to follow esthetical guidelines. All programs proceed on input being composed of the three-dimensional ligand and receptor coordinates. Due to the lack of guiding principles, the algorithms and resulting diagrams of the different available tools substantially differ in graphical styles, level of detail, and information content.