For example, to generate an images like the one which I have attaced
I would suggest,
- NGL viewer: http://nglviewer.org/ngl/?script=showcase/ferredoxin
- LiteMol: https://www.litemol.org/Viewer/
But, I personally prefer VMD over online apps. Chimera is also a good alternative.
I'd say that image was prepared using Pymol. You can also try VMD or Chimera as already mentioned. However, they are not online tools, you should download them.
Hi Harindu
You can try "Hex" for protein Protein interaction. There are many others such astry AutoDock, Pymol, or Chimera (for better resolution).
Good luck
Junaid Furhan Madhuranga Rathnayake Vitor Rabelo
thank you very much
For a more detailed analysis of the interaction, including PyMOL visualisation, I would recommend PLIP https://projects.biotec.tu-dresden.de/plip-web/plip
Harindu Rajapaksha
I will suggest https://www.playmolecule.org/
also what Annemarie Honegger mention is so good .
You can try Ligplot+ for the interactive interaction analysis.
https://www.ebi.ac.uk/thornton-srv/software/LigPlus/
This will provide you with better result.
On my personal opinion, I prefer Chimera UCSF interactive visualization with link: https://www.cgl.ucsf.edu/chimera/
(Freedownload). Then, you can active the graphics quality (Multisample). This is a good idea to analyze image files to .pdb format
I routinely make such images with DeepView (https://spdbv.vital-it.ch/), in the control panel you can select separately for each amino acid and ligand how it is displayed: backbone only, side chain as ball and stick or van der Waals, or ribbon, with or without a label. It can also create 3D-images, either in blue/red or in side-by-side.
The program is free (as in beer), unfortunately, further development seems to have stopped.
Hi Harindu Rajapaksha
PyMol, Chimera are best option for your query but JAVA based LigPlot (https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/) tool also generate publication quality interaction images.
If you use Ligplot, try LigPlot+
https://www.ebi.ac.uk/thornton-srv/software/LigPlus/
It incorporates major updates:
Quote:
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:
Getting such a picture generally requires the user to visualize the structure of interest with a software like pymol, chimera... if you are searching an automatic tool you can try Ligplot as previously mentioned
Hello Harindu Rajapaksha
Pymol from Schrodinger, is one of the best Software for visualizing ligand-protein interactions, that is used and preferred by many researchers. You have options in the software to export the visualizations into High-definition publication quality images. Besides, the image uploaded by you is also an example of Pymol generated image, in which the protein molecule is made transperent, and the interacting residues as well as the ligand are being highlighted and labelled. All these operations can be performed easily using Pymol.
The latest version is Pymol 2.4, and it can be downloaded and used from the following link:
https://pymol.org/2/
Hope it helps.
Hi....
Chimera and JAVA based LigPlot (https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/) tool generate publication quality images.
Dr Swarna Kanchan please can you put me through on how to use Chimera or I would appreciate any video tutorial. I need to visualize my docking output.
Protein-ligand interactions profile webpage and protein-plus webpage
discovery studio will give us best pics along with all the other interactions which u wont get in chimera also. When u open the file in chimera, first save it in pdb format. then open it in discovery studio. Select any best pose and then look for the interactions. U will get very nice pics for publication quality
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