Hi!!

well, for analysis of docking you can use Pymol

Hello,

Almost every docking calculation software offer this... However, I frequently use LigandScout... It is very good in-pocket visualization tool, especially if protein-ligand complex is available...

Hello,

Chimera is also a very good for visualization.. provides good quality images, and its freely available.

i am using as said Mr.Shubhandra Tripathi, but it appears black and white in color. there is a chance for changing colors like RGB. May i choose any color for the clear visualization?

I suggest Pymol. It is the best visualization program and useful to make figures for publications.

There are many more open-source and commercial softwares available but as the open-source is valuable I have used Molegro Virtual Docker(MVD).

It is an open-source useful tool for visualizing protein-ligand interactions. You can label each interacting amino acids at active site or binding pocket, measure rmsd values between protein and ligand and also useful to devlope an interaction map if you need. So you can use this software for better visulization of docking results which can publishable. 

Another, open-source software called CLCbio workbench (http://www.clcbio.com/products/clc-drug-discovery-workbench/) have best graphics for visualization of protein-ligand docking.

Chimera , VMD, Maestro . 

PyMol for 3D representation and ligplot+ for docking interaction in 2D. Both will generate easily 600dpi images.

you can also use DS visualizer 3.5 or 4 which is free and very is easy to use also provides good quality images for publications

Pymol will give you best figures.

Thank you to all for your valuable answers. The answers helpful to complete the assignment now.

by

T. karthick

Good to know Karthick. May I know which tool did you finally use to complete the assignment??

Dear Prashantha Karunakar

i used UCSF Chimera for visualization. It clearly indicates the hydrogen bonding between ligand and the active residues of protein.

You can also use CLC drug discovery workbench, which give you best visualization.

http://www.clcbio.com/products/clc-drug-discovery-workbench/

Hi you can also use VMD and Discovery studio for visualisation

 How to get nice pictures from Discovery studio for publications, can any elaborate please ?

Please share some relevant articles / protocols... Thanks & Regards

I would prefer Discovery Studio Visualiser. U can get figure quality of even very high resolution

I think with my point of view Discovery Studio is the best option. You will get quality figures with quite better resolution as compared to other for your publication.

I am having some challenges viewing my ligand-protein interaction using Discovery Studio. It keeps telling me 'A receptor molecule containing amino acid or nucleotide is required. The defined receptor molecule contains no amino acids or nucleotides. Please select an appropriate receptor molecule using the Define Receptor tool panel command', this is even when the receptor is defined. I have attached the image. What's the way out. Thank you.