I would go to the Protein Data Bank, and look for protein structures that include berberine as a ligand:
-- http://www.rcsb.org/pdb/results/results.do?qrid=C21BC50D&tabtoshow=Current
On Wednesday, August 6, 2014 6:27:00 AM UTC-7, Mega [Andreas Stuermer] wrote:
Unfortunately, there's not that many of those, so you may also want to check some other berberine related compounds. Alternatively, you can start from the proteins that are associated with cbl-ubiquitin ligase, check what ligands those bind, and if there is something similar to berberine in there (there's a variety of metrics to measure how similar in structure two small molecules are). There may also be some other databases out there with known protein - small molecule interactions, that don't require a protein structure.
There's various pathway databases to retrieve genes that are in some way associated for your gene of interest. I like STRING, because it also includes gene coexpression data, genomic context, and co-citations:
http://string-db.org/
Good luck!
Patrik
On Wednesday, August 6, 2014 6:27:00 AM UTC-7, Mega [Andreas Stuermer] wrote:
Hi!Could use some help with the following:One mode of action is that berberine and derivates activate cbl-ubiquitin ligase. Now I was told to identify structures where berberine binds to. So maybe to cbl, or some upstream protein.
I don't know of any bioinformatic tool that is advanced enough to solve this. Does anyone know of one?Best,Andreas
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