Receiving Helpdesk

ligplot plus

by Tavares Thiel Published 3 years ago Updated 2 years ago

How to use ligplus with LIGPLOT +?

If you are using the Windows version, then double-click the executable jar file named “LigPlus”. Prepare a PDB file of a protein-ligand complex as an input to LigPlot +. You can use Pymol for this as shown below: Choose an appropriate pose of the ligand. This will save your protein-ligand file in PDB format. Here, we have saved it as ‘ input.pdb ‘.

What's new in The LIGPLOT+ suite?

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.

How do I run LIGPLOT + on Ubuntu?

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

How can I view a LIGPLOT diagram in 3D?

The 3D representation of any LIGPLOT diagram can be viewed in either PyMOL or RasMol with all the interactions indicated. A RasMol 3D view of the ligands in the first example above, superposed in 3D (click image to expand).

What is LIGPLOT plus?

Groups Thornton Software > Ligplot+ 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.

How do I install LIGPLOT Plus on Windows?

On a Windows machine, double-click on LigPlus. jar in the LigPlus directory (or on the shortcut icon on your Desktop if you've set one up). When the program has loaded you will see the starting LIGPLOT+ window. See the Operating Manual for instructions on how to generate a LIGPLOT/DIMPLOT diagram.

How do you reference a LIGPLOT?

Wallace A C, Laskowski R A & Thornton J M (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions.

What is protein-ligand interaction?

Interactions. The protein-ligand complex is a reversible non-covalent interaction between two biological (macro)molecules. In non-covalent interactions there is no sharing of electrons like in covalent interactions or bonds.

How do I download Ligplot?

Download licence file and programs Save the zip file on your system and then follow the Installation Instructions to install. The software licence is valid for 1 year from today. When it expires, simply return to this page and download a new version of the software.

What is molecular docking studies?

Molecular docking is a kind of bioinformatic modelling which involves the interaction of two or more molecules to give the stable adduct. Depending upon binding properties of ligand and target, it predicts the three-dimensional structure of any complex.

How do you cite Pdbsum?

PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank....PDBsum.ContentAuthorsRoman Laskowski & al. (1997)Primary citationPMID 9433130AccessWebsitewww.ebi.ac.uk/pdbsum/8 more rows

What is KD drug?

KD is determined experimentally and is a measure of the affinity of a drug for a receptor. More simply, the strength of the ligand–receptor interaction. To determine KD, a fixed mass of membranes (with receptor) are incubated with increasing concentrations of a radioligand until saturation occurs.

How do ligands bind to proteins?

A ligand is a small molecule that is able to bind to proteins by weak interactions such as ionic bonds, hydrogen bonds, Van der Waals interactions, and hydrophobic effects. In some cases, a ligand also serves as a signal triggering molecule. A ligand can be a substrate inhibitor, activator or a neurotransmitter.

What is docking score and binding energy?

Binding free energy is the sum of all the intermolecular interactions that is present between the ligand and the target. 2. Docking Score is the scoring function used to predict the binding affinity of both ligand and target once it is docked.

Audience

Labs and researchers interested in a solution to create and visualize ligand-protein interaction diagrams

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How to generate config file for docking using Autodock Tools?

A configuration file is one of the required files for docking using Autodock Vina. In this article, we are going to generate a config file using Autodock Tools GUI [1]. (more…)

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