Crystallographic Structure (not the 3d picture)

Philipp Pagel philipp.pagel at gmx.de
Mon Mar 1 16:12:11 EST 2004


Giuseppe Torelli <joseph1900 at interfree.it> wrote:

> I need the crystallographic structure
> of a protein given its amino acid sequence.
> I don't mean the 3D picture but the assigment
> of each amino acid residue in a given structure.
> May someone of you tell me a web link or something else ?

You are looking for PDB:

http://www.rcsb.org/pdb/

I don't think you can directly search by sequence at their site, but of
corse you can download the dataset and run your BLAST locally. If this
sounds like too much hassle - e.g. if you only want to use this
occasionally you can try one of these:

http://xcc.life.nthu.edu.tw/blast_new/blast/blast_pdb.html
http://www.rtc.riken.go.jp/jouhou/HOMOLOGY/dbsearch/pdbblast/
http://gibk26.bse.kyutech.ac.jp/jouhou/HOMOLOGY/dbsearch/pdbblast/

If you are talking about *predicting* the 3d structure the situation is
less easy: There are plenty of bright people out there who are trying to
solve that problem. While some solutions look promising, none even comes
close to an actual crystal structure...

cu
	Philipp

-- 
Dr. Philipp Pagel                           Tel.  +49-89-3187-3675
Institute for Bioinformatics / MIPS         Fax.  +49-89-3187-3585
GSF - German National Research Center for Environment and Health
Email: p.pagel AT gsf . de
http://mips.gsf.de/~pagel




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