When comparing wild-type and mutant proteins, LigPlot can visually demonstrate how a mutation (e.g., changing a Threonine to an Alanine) might remove a critical hydrogen bond, explaining a loss in binding affinity or catalytic activity.

LIGPLOT performs a geometric analysis to detect non-covalent interactions:

LigPlot calculates potential hydrogen bonds based on distance and angle criteria between hydrogen donors and acceptors.

Understanding a LigPlot diagram requires recognizing its standard visual language:

The software simplifies the interpretation of molecular docking results by distilling thousands of atomic coordinates into a single, high-level map.