How to Make a 2D Interaction Diagram for Docking (Free Tools)

By BioDockify Computational Research Team · September 3, 2026 · Tutorials

Make 2D ligand interaction diagrams for docking results with free tools: DS Visualizer steps, LigPlot+ schematics, PLIP verification and figure conventions.

Read the complete article with tables, code and references on BioDockify.

Key References

• Laskowski RA, Swindells MB. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model. 2011;51:2778-2786. doi:10.1021/ci200227u
• Salentin S et al. PLIP: fully automated protein-ligand interaction profiler. Nucleic Acids Res. 2015;43:W443-W447. doi:10.1093/nar/gkv315
• BIOVIA Discovery Studio Visualizer documentation, 3ds.com.

Scope & Limitations

2D diagrams summarize a single pose; they say nothing about pose population or binding free energy