LigPlot+: A Tool for Visualizing Protein-Ligand Interactions
LigPlot+ is a software that can plot schematic diagrams of protein-ligand interactions, based on the LIGPLOT and DIMPLOT programs[^1^] [^2^]. It can also generate 3D molecular models of the complexes and superpose them for comparison. LigPlot+ is a graphical front-end that allows users to interactively edit, manipulate and print the plots. LigPlot+ can be used for drug discovery and analysis of protein-ligand complexes.
To download LigPlot+, you need to apply for an academic licence from the European Bioinformatics Institute (EBI) website[^1^]. You will receive a password to access the download page, where you can download a zip file containing the licence file and the programs for Linux, Windows or Mac OS X. The licence is valid for one year and can be renewed by downloading a new version of the software. You also need to have Java installed on your system to run LigPlot+.
For more information on how to use LigPlot+, please refer to the operating manual[^1^] and the original publications[^3^] .
Select the PDB file and the ligand of interest from the main window.
Click on the LIGPLOT button to generate a plot of the ligand-protein interactions.
Edit the plot as desired using the mouse and the menu options.
Save the plot as a PostScript file or export it as an image file.
Optionally, view the 3D representation of the plot in PyMOL or RasMol.
Optionally, superpose related plots to compare different complexes.
For more details on each step, please refer to the operating manual[^1^] [^3^].The main window of LigPlot+ looks like this:
From here, you can select the PDB file and the ligand of interest from the drop-down menus. You can also specify the plot parameters, such as the H-bond distance and angle cutoffs, the contact distance cutoff, and the plot title. You can also choose whether to include water molecules, metal ions, and cofactors in the plot.
The menu options for editing the plot are:
File: allows you to save, print, or export the plot.
Edit: allows you to undo, redo, cut, copy, paste, or delete elements of the plot.
View: allows you to zoom in, zoom out, fit to window, or show grid lines.
Plot: allows you to change the plot type (LIGPLOT or DIMPLOT), superpose related plots, or view the 3D representation in PyMOL or RasMol.
Tools: allows you to add missing H-bonds, remove unwanted H-bonds, change the colour scheme, or change the font size.
Help: provides access to the operating manual and the about information.
To superpose related plots, you need to have two or more plots open in separate windows. Then, you can select Plot > Superpose plots from the menu bar of any window. A new window will appear with a list of all open plots. You can select which plots you want to superpose and click on OK. The program will then attempt to align the plots based on their 3D coordinates and display them in a new window. You can then edit the superposed plot as usual. 0efd9a6b88