protein-ligand docking visualization using NGLViewer

usegalaxy.eu support
1

activesite
Hello,
I was following the tutorial at Protein-ligand docking.
I am not able to visualize my results as per the tutorial and as per attachment using NGL Viewer.
Can you please help me?
regards
Preenon Bagchi

2

Hello,
I was following the tutorial at Protein-ligand docking.
I am not able to visualize my results as per the tutorial and as per attachment using NGL Viewer.
Can you please help me?
regards
Preenon Bagchi

3

Answered on gitter / matrix.

2 Likes
4

Because it seems people are still reading this thread, this is what I wrote to Preenon:

we created that GIF by combining screenshots from two poses together
if you got as far as creating the PDB files for the docked poses, you can click on the Visualize this data button on the datasets in your history
then you have a choice of visualizations and you can pick NGLviewer

2 Likes
5

Hi Simon,
I am learning protein-ligand docking by following the galaxy training with Hsp90 as a model. I successfully obtained a list of docked ligands. However, I cannot visualize the interactions between those ligands and their receptor (Hsp90) by NGL Viewer. I tried to input the docking files to AutoDockTools (Analyze → Dockings → Show Interactions) but failed. It seems to me the output files obtained from Galaxy do not have any information about the interactions. Am I right? Are there any ways to compute the docking on Galaxy to have output files with protein-ligand interactions that can be visualized using AutoDockTools? I look forward to hearing from you.
Many thanks,
Trong Tran