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LigPlot+: A Tool for Visualizing Ligand-Protein Interactions
If you are interested in studying the molecular interactions between ligands and proteins, you may want to use a tool that can generate 2D diagrams of these interactions. One such tool is LigPlot+, which is a successor to the original LIGPLOT program developed by the Thornton group at EMBL-EBI. LigPlot+ is a free software that can be downloaded from the EMBL-EBI website after obtaining an academic licence. In this article, we will introduce some of the features and benefits of using LigPlot+ for visualizing ligand-protein interactions.
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What is LigPlot+?
LigPlot+ is a Java-based program that can automatically generate 2D diagrams of ligand-protein interactions from 3D structures. The diagrams show the ligand and the protein residues that interact with it via hydrogen bonds or non-bonded contacts. The program also displays the distances and angles of the hydrogen bonds, as well as the solvent accessibility and hydrophobicity of the residues. The diagrams can be edited on-screen using mouse click-and-drag operations, and can be saved as image files or vector graphics files.
What are the advantages of using LigPlot+?
LigPlot+ has several advantages over the old version of LIGPLOT, as well as other similar tools. Some of these advantages are:
LigPlot+ can superpose or split related diagrams. This means that you can compare the interactions of different ligands with the same protein, or different proteins with the same ligand. The program will highlight any conserved interactions in red, which can help you identify key residues or binding motifs. For example, here is a superposed diagram of two ligands (imatinib and nilotinib) binding to human c-Abl tyrosine kinase:
LigPlot+ includes an improved version of DIMPLOT, which can plot protein-protein or domain-domain interactions. You can select the interface of interest and DIMPLOT will show you the residue-residue interactions across the interface. You can also display the residues in one of the interfaces in sequence order, which can help you see the patterns of interactions. For example, here is a DIMPLOT diagram of the protein-protein interface between chains B and C in a streptavidin mutant:
LigPlot+ can link to PyMOL or RasMol, which are popular 3D molecular visualization programs. You can view the 3D representation of any LigPlot+ diagram in either PyMOL or RasMol, with all the interactions indicated. This can help you better understand the spatial arrangement and geometry of the interactions. For example, here is a RasMol 3D view of the superposed ligands in the first example above:
How to use LigPlot+?
To use LigPlot+, you need to download the zip file from the EMBL-EBI website and install it on your system. You also need to have Java installed on your system. The installation instructions are available on the website. Once you have installed LigPlot+, you can run it by double-clicking on the LigPlus.jar file or by typing java -jar LigPlus.jar in a terminal window. You will see a graphical user interface that allows you to load a PDB file or a list of PDB files, select a ligand or an interface, and generate a plot. You can also edit the plot using various options and menus. For more details on how to use LigPlot+, please refer to the operating manual.
LigPlot+ is a useful tool for visualizing ligand-protein interactions in 2D diagrams. It has several features that make it superior to other similar tools, such as superposition and splitting of related diagrams, improved DIMPLOT module, and links to PyMOL and RasMol. LigPlot+ is free for academic use and can be downloaded from the EMBL-EBI website. If you are interested in studying the molecular interactions between ligands and proteins, you should give LigPlot+ a try.
Laskowski R A, Swindells M B (2011). LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model., 51, 2778-2786.
LigPlot+ home page - EMBL-EBI
LigPlot+ academic licence - EMBL-EBI
LigPlot+ download - Version 2.2 - EMBL-EBI
PDB entry 1swo
PDB entry 2hyy
PDB entry 3cs9
LigPlot+ installation - EMBL-EBI
LigPlot+ operating manual - EMBL-EBI
LigPlot+ home page - EMBL-EBI