Ligplot Instant

ligand-protein interaction diagrams - LigPlot + v.2.3 - EMBL-EBI

A significant challenge in 2D visualization is avoiding the overlap of residues. LigPlot employs a layout algorithm that attempts to arrange the interacting residues around the ligand in a way that minimizes clutter and crossing lines, ensuring the diagram remains legible even for large binding sites. ligplot

Figure 1 (conceptual): A LIGPLOT of the HIV-1 protease inhibitor indinavir. Hydrogen bonds are green dashed lines; hydrophobic contacts are red arcs; the ligand is in thick black bonds. ligand-protein interaction diagrams - LigPlot + v

| Limitation | Explanation | |------------|-------------| | No π-π or cation-π stacking | These are treated as hydrophobic contacts, losing directional detail. | | No metal coordination | Interactions with metal ions are not specially marked. | | No halogen bonds | Not detected in original algorithm. | | Static 2D layout | May produce overlapping residues for very crowded binding sites. | | PDB format dependent | Requires correct CONECT records for ligand bonding. | Hydrogen bonds are green dashed lines; hydrophobic contacts

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

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