High Throughput Screening for ligands in case of known protein-protein binding complex

Question

[saptarshi.mukhopadhyay2014]

Hello,

I am trying to screen for ligands that will act as antagonists in a protein-protein complex. So the basic idea is to use the antagonist to inhibit the complex to form. My initial idea is to understand and analyze the protein docking complex and then further go for docking it with a ligand (Its a Ag-Ab complex). 1) What all resources do I have at my disposal for analyzing the Ag-Ab docking? 2) How do I use the information of the binding site of the protein complex and use that information to find a pertinent ligand that will bind in perfectly? 3) How do I screen for a ligand if no known ligand is found against the Ag-Ab complex, to go for docking?

Thanks!

Regards, Saptarshi

Answer 1

[Ram]

I think these threads may be helpful for you :

Ligand Docking In The Minimized Protein.

Protein Protein Docking