Reagents etc.

If you are interested in using any of the compounds we have reported (e.g. azobenzene-based cross-linkers), please send us an email. We normally share these, or provide them at cost, to academic researchers.

sGAL

sGAL is a computer program designed to find pairs of sites suitable for
introducing intramolecular chemical cross-links into proteins. sGAL takes a protein
structure file in PDB format as input, truncates each residue sequentially to its gamma
side chain atom to mimic mutation to Cys, and calculates the exposed surface area of the
gamma atom. The user then inputs the minimum and maximum lengths of the crosslinker.
sGAL provides as output pairs of residues that would have exposed gamma atom
separations that fall within this range. Furthermore, if a line joining the pair of gamma
atoms contacts more than a given number of buried atoms, that pair is discarded. In this
way, sites for which the protein would sterically interfere with cross-linking are avoided.

Credits: En-Shuin Lee, Fuzhong Zhang, Zhen Qi Lu

See: Bioinformatics. 2006, 22(24):3101-2

For a zip archive: sGAL.zip

Installation: Download the zip file from the link given above. Unzip. Make sure sGAL.jar, AutomateSurfaceRacer.vbs, and surfrace5_0.exe are
in the same folder under C:\sGAL\

To run close all other applications (may not be necessary depending on what
you have running) enter the form and click submit,