LigPlot⁺ v.2.2 - ligand-protein interaction diagrams

LigPlot⁺ is a successor to our original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.

In addition to the new interface, the program includes several major enhancements over the old version:

1. Superposition of related diagrams. When two or more ligand-protein complexes are sufficiently similar, LigPlot⁺ can automatically display their interaction diagrams either superposed or side by side. Any conserved interactions are highlighted (see example below). More examples can be found in our original publication (below), as well as here.

   Overlaid plots

   Split plots

   Binding sites of two structural models of the same protein complexed with two different ligands (click to enlarge). The protein is human c-Abl tyrosine kinase, and the two ligands are imatinib (PDB entry 2hyy) and nilotinib (3cs9). The ligands and protein side chains are shown in ball-and-stick representation, with the ligand bonds coloured in purple. Hydrogen bonds are shown as green dotted lines, while the spoked arcs represent protein residues making nonbonded contacts with the ligand. The red circles and ellipses indicate protein residues that are in equivalent 3D positions when the two structural models are superposed.

2. Improved DIMPLOT program. The LigPlot⁺ suite also now includes an update of the original DIMPLOT program for plotting protein-protein or domain-domain interactions. Users can flexibly select the interface of interest and DIMPLOT will then generate a diagram showing the residue-residue interactions across the interface. To assist in interpretation, the residues in one of the interfaces can be optionally displayed in sequence order. Note that the DIMPLOT module does not yet allow multiple plots of related interfaces.

   DIMPLOT interface diagram

   Residue-residue interactions across the protein-protein interface of chains B and C in PDB entry 1swo (a streptavidin mutant). Click to enlatge).

3. Links to PyMOL and RasMol. The 3D representation of any LIGPLOT diagram can be viewed in either PyMOL or RasMol with all the interactions indicated.

   RasMol 3D view

   A RasMol 3D view of the ligands in the first example above, superposed in 3D (click image to expand). The ligands are shown with thick stick, while the residues interacting via H-bonds are shown as thin sticks. H-bonds are shown in cyan. The dotted surfaces correspond to the parts of residues that inter4ct with the ligand via non-bonded contacts only.

Reference

Availability

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Last modified: 13 Jul 2012