I am docking a ligand in a protein scaffold using PyRx but after docking, I need its coordinates. It will be very helpful if I could know how to get the coordinates of the docked structure.
- Thank You
Arindam
Arindam Paul Hi
Hope you doing well
first of all, before performing docking in pyrx set your coordination as per literature. But you want to do blind docking so after docking export your complex and open it in the DS visualizer and you can find the coordinate there.
Use BIOVIA Discovery Studio
Load the complex and select the ligand
Then under "Receptor-Ligand Interactions" section click on "Define Site" (Click "From current selection")
This will form a bubble in the ligand site
Select the bubble (will appear yellow in colour)
Right click on the bubble and and click Attributes of SBD_Site_Sphere
It will open a window showing your coordinates
- Badges
- Science topic
- Similar topics
- Filing