Simulation-Based Algorithm for Two-Dimensional Chemical Structure Diagram Generation of Complex Molecules and Ligand–Protein Interactions

Computer
programs for structure diagram generation (SDG) are indispensable
cheminformatic tools that translate one- or three-dimensional (1D
or 3D) chemical structure data stored in electronic formats to human-readable
2D depictions. Although many such programs are known, only a moderate
part of chemical space can be handled by existing algorithms. For
many classes of natural and synthetic compounds the results obtained
with current SDG methods are illegible. A new algorithm based solely
on a physical simulation of a molecule has been developed. The method
allows for a general and global approach to avoid overlapping atoms
and substituents. While the algorithm shows no advantage for trivial
molecules, it shows superior performance over existing methods in
depicting the most challenging compounds. The algorithm can generate
chemically correct and legible 2D structure diagrams of many classes
of natural and synthetic compounds that are intractable with existing
SDG algorithms. The use of the method for generating schematic ligand–receptor
interaction diagrams is also discussed.