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You may use similarity to known ligands to find potential binding partners in the PDB.
Try a ligand similarity search for your ligand:
http://www.rcsb.org/pdb/search/advSearch.do
From the menu, choose “Chemical Structure” and draw your ligand. Then select “Search Type: Similar”. This search will return PDB entries with ligands that are
chemically similar to your ligand.
Peter Rose,
RCSB PDB
From: CCP4 bulletin board [mailto:[log in to unmask]]
On Behalf Of L
Sent: Monday, October 14, 2013 4:53 AM
To: [log in to unmask]
Subject: [ccp4bb] Ligand binding protein partner search
Hi all,
I'm looking for a way to find/predict protein partner(s) for our ligand (small chemical; MW<500 Da).
There're lots of servers and softwares to find/predict a ligand with known protein structure, but hardly find a way to discover potential protein partner(s) with known ligand.
That would be great if anyone give me a clue. Web server, software, any suggestion are all appreciated.
Thank you
L