[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
Re: [ccp4bb] Ligand binding protein partner search
It's definitely possible to rig, say, autodock to run the same small molecule over every protein in the PDB. Results, of course, should be taken with a grain of salt. On Mon, 2013-10-14 at 20:53 +0900, L wrote: > 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 -- "Hurry up before we all come back to our senses!" Julian, King of Lemurs
Re: [ccp4bb] Ligand binding protein partner search
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
Re: [ccp4bb] Ligand binding protein partner search
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 > 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 >
