how to find binding sites - (Aug/25/2007 )

Hi

I have a protein (only amino acid sequences, no structural data is avalable) and I wand to find the binding partners wich probably bind to my protein. I will be appreciating if some body of you could guid me to the bioinformatic tools can be used for this purpose... thanks alot

hemin

You might have to do the experiment. Purify your protein, prepare antibodies against it, attach these to beads (probably use protein A Sepharose) then pass cell lysate over the beads. Your protein will stick to it, and any binding partners will be isolated. You can then identify the binding partners.

Simple to write, not so simple to do... but that's why we are called researchers.

for human proteins, you can check the results of some high-throughput screenings, which are listed in the Gene section of NCBI (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene) or in the human protein reference database (http://www.hprd.org/). Beware, a lot of this data is not confirmed, but it may be a start.

one of this program could be helpful

good luck!

biotools