have a look at this paper and the references.

Using fragment cocktail crystallography to assist inhibitor design of Trypanosoma brucei nucleoside 2-deoxyribosyltransferase. J Med Chem (2006) vol. 49 (20) pp. 5939-46

The SEC after soaking is a bad idea, you will loose your fragment as it is most likely a low micromolar binder. A better way to approach this is to use a filtration device say with 3 kDa cutoff. Concentrate your protein + ligands and in a separate tube just the ligands without protein. Then run both samples over a mass spec and see if you can detect a specific decrease in one or more of your ligands.

Jürgen

P.S. wasn't sure what you mean by biological relevant DeCode has a library called Fragments of Life, otherwise Zenobia is not bad.

On Oct 27, 2009, at 10:58 AM, c.weinert wrote:

Dear all.

I am looking for a library of small (biologically relevant) compounds to
test binding to a protein. Does somebody know, if there is a company
that sells such a library for fragment based library screening? (to a
reasonable price).

And does anybody has experience with screening such libraries? I assume
that one approach would be soaking the protein with the compounds,
followed by SEC and MS analysis. Anybody tried directly soaking crystals
followed by X-ray analysis?

Thanks alot already in advance for your help.

Sincerely,
Christopher

Jürgen Bosch

Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/