I'm performing docking with Autodock Vina.
The out file and the log file were retrieved.
Now I want to visualize the residues involved in the interaction with the ligand.
Hi Nantenaina,
You can visualize the protein-ligand interactions using Pymol, Ligplot or Discovery studio visualizer software (need to request the license from the team).
All the best,
Rajesh
You can visualize the Protein-Ligand interactions using Maestro, Pymol, DSV. These visualizers are free for academics.
Thank you all.
Rajesh Durairaj
I've tried to open the out file with the protein using Pymol and tried to save it as pdb file in order to visualize the interaction in Ligplot but it doesn't work.
You can try Biovia Discovery Studio Visulaizer for free.However there are quite other good one's too but I have tried with DS Visualizer. I found it awesome and I think you can easily visualize the residues.
Load receptor.pdb and ligand.out file together on PyMOL. Visualize and Save best binding pose.
In my opinion the easiest way to visualized the docking results is to upload the ligand-receptor complex, or the best ligand pose and the pdb file of the receptor in separate, to the Discovery Studio Visualizer Software (BIOVIA, Dassault Systemes). The interface is pretty easy to work with and the image graphics are excellent.
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