I have to visualize the interactions (Van der Waals, electrostatic, etc) within a protein. But I don't know how to perform this in discovery research studio. Thank you in advance!
1- Open your complex by clicking file > open
2- Select your ligand in 3D scene and click on "Define Ligand" at "Receptor-Ligand interactions" tab, as shown in Fig1.
3- Once your ligand is defined, click on "Show 2D diagram", so you will have a 2D diagram of protein-ligand interactions. (Shown in Fig2)
You can also explore their interactions within the 3D scene by clicking on the arrow next to "Non-bonding interactions" > "Interaction option" to check any interaction you want, their distance and/or type. (Shown in Fig3).
Hope it helps.
In discovery studio, go to tools >> Receptor-Ligand interactions >> View interactions >> show receptor-ligand interactions on a 2D diagram >> Show 2D diagram.
Regards
open discovery studio, go to tools >> then from the options select Receptor-Ligand interactions >> then View interactions >> then select the option show receptor-ligand interactions on a 2D diagram >> Show 2D diagram.
You can also use an academic version of Maestro or Ligplot+ for the same.
Aviola Mehmeti,
To visualize interactions within a protein - Open required protein PDB file goto structure option, open the drop-down list from the monitor, select option Non-bond interactions, finally choose option/options for interaction types, and do other settings & click ok button.
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