In our last article, we explained the installation of LigPlot⁺ [1] on Ubuntu. In this article, we will perform protein complex analysis using LigPlot⁺. 

Please refer to our last tutorial for executing LigPlot⁺ on Ubuntu. If you are using the Windows version, then double-click the executable jar file named “LigPlus”.

Preparing input

Prepare a PDB file of a protein-ligand complex as an input to LigPlot⁺. You can use Pymol for this as shown below:

1. Open Pymol --> File --> Open --> Select .pdb file of protein
2. Go to File --> Open --> Select output file of docking
3. Choose an appropriate pose of the ligand.
4. Go to File --> Export Molecule --> Select 'PDB Options' --> Select 'Write CONECT records for all bonds'
5. Click 'Save' --> Change 'Save as type' to 'PDB' --> Click 'Save'

This will save your protein-ligand file in PDB format. Here, we have saved it as ‘input.pdb‘.

Analyzing on LigPlot⁺

After opening LigPlot⁺, follow the steps mentioned below:

1. Go to File --> Open --> Browse --> Select 'input.pdb' file. It will display how many ligands and chains this protein-ligand file contains. You can also select a range of residues for analysis including several other options.
2. It also displays DIMPLOT and Antibody tabs but in this article, we are dealing with LigPlot only.
3. Click 'Run'

It will display a 2D plot showing interactions between the protein and ligand. You can select different colors, and move atoms or residues, and so on.

References

1. Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein engineering, design and selection, 8(2), 127-134.