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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of L Sent: Monday, October 14, 2013 4:53 AM To: CCP4BB@JISCMAIL.AC.UK 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
