I am working on a protein-ligand molecular docking techniques. And am stuck in the process of generating 2d as well as 3d protein-ligand interaction images. I tried using LigPlot and Pymol for 2d & 3d images respectively, but the results are not matching. So i also want to know whether it is human error by me or some software issues. The images are attached herewith for you to know the issue. Amino acid Met42 in 3d image is not correlating with amino acid Val35 in LigPlot. I tried generating the 3d interaction in PLIP webserver as well even there Met42 is having H-bond with protein.
So, is the LigPlot output is showing false results?
For 2D, I recommend you use Discovery Studio. But for 3D, ChimeraX is the best I've ever used.
Hi Vishal Chanda
Always keep in mind that each software calculate interactions differently, thus generating different results.
You have the option to change the interaction calculations via the preferences option available on LigPlot.
I recommend to at least read the basic manual of the software you are using to avoid any unnecassary frustration and confusion in the future.
Hope this help. All the best.
Thank you so much Nor Farrah Wahidah Ridzwan & Mokhamad Fahmi Rizki Syaban had been confused for quiet a long time without knowing this. I will do the needful and try generating the interactions.
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