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Hi, Predict_FX has worked quite well in our hands for that purpouse but you have to pay for a licence. It is currently commercialized by Certara: http://www.certara.com/products/molmod/predictfx Regards, Zsolt Böcskei sanofi Paris 2013/10/14 Rose, Peter <[log in to unmask]> > 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 **** >