I have docked two protein in order to comprehend the residue involve in PPI interaction. Now, I want to visualise detailed interaction types and bonding pattern.
I have tried Discovery studio, PyMol but failed to depict protein-protein interactions (however they can handle ligand-protein).
Is there any other way to demonstrate it?
The free academic version of maestro: https://www.schrodinger.com/maestro
can help you display the interaction diagrams of the amino acids, interacting with each other in the cross-linking interface of the two protein; if you select these residues of this interface, it will show the connections.
PyMOL is a loyal servant. If you tell PyMOL what you want, in a language that PyMOL understands (the language of two snakes), PyMOL will do it without fail or hiss.
PyMol is no doubt one of the best software for visualization...but lately i have been using Chimera for P-P and P-L in teractions and i found it far better in terms of graphics and quality of the image. You can give it a try Athar. If you are using it for the first time then i will suggest you to refer to its manual coz its quite tricky at first.
PyMol would be a good option!
You can follow the protocol here for tracing protein-protein interactions.
https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts
i recommend using maestro because it shows a variety of interactions (H-bonds Pi stackings good contacts )
The free academic version of maestro: https://www.schrodinger.com/maestro
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