I have a pdb file of a protein and a small molecules, respectively and I want to get a diagram like this figure, but I don't know how can I do it. I ask for your help if you have used this software.
You can download ligplot+, which is a GUI based tool for ligplot. (https://www.ebi.ac.uk/thornton-srv/software/LigPlus/)
There's an other tool called Poseview, which PDB uses show ligand interactions with Protein residues (http://poseview.zbh.uni-hamburg
Dear friend,
Lig Plot has a so simple process Save protein and ligand in two separate pdb file then load this files into the program.
best,
HHA
As far as i have used the LIGPLOT,
I got the docking result in PDB file, either from autodock or form Patchdock, or anyother docking software.
First get the docking done. Ligplot is just a tool to view the docking result. It does not provide any docking facility. So, first dock your protein and ligand in any docking tool and then u can view the result in LIGPLOT.
While loading the result PDB file in Ligplot, you would have to choose the correct ligand to view, for eg., if your Ligand's 3digit code is 3AU or something, then choose that one, cause Ligplot displays all possible ligand like molecule associated with your protein.
Good Luck.
ِDear Guilherme Oliveira Quintino
how can generate 2D interactions diagram via Discovery Studio Visualizer? what are the steps?
I used it but the interactions shown in Discovery Studio Visualizer are less than those predicted in LigPlot+. can you help me?
Can we generate such figures for protein-protein interactions. I mean instead of a ligand-protein complex can we use a receptor-protein complex.
Is there a software for studying this as well?
You can use ligplot+ or discvery studio or chimera for visualisation and h-bonded interactions.
Thanks.
But, I was looking for softwares for studying protein-protein interaction not ligand-protein interaction.
Apart from Chimera, you can also use DIMPLOT. The improved presentation of protein-protein interactions is now possible with DIMPLOT (An improved version of LigPlot). You can download it following some simple set of instructions on https://www.ebi.ac.uk/thornton-srv/software/LigPlus/
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