Dear Jacob, I have developed a structural conservation function in MANORAA.org that acts by using ligand's rigid fragment as a probe to see what protein's active site residues retain its position relative to the ligand in gradient colours.
For example, with staurosporine as a query molecule. http://mahori.icbs.mahidol.ac.th/Manoraa/sstq/ligandquery.php?queryby=lig&lignum=STU You can input the atoms of the ligand that you want to use for superpositioning. It will browse through the whole protein databank to find the PDB structure to find all the binding partners and often including their structural homologs. Is that what you are trying to do? Sincerely, Duangrudee Tanramluk ------------------------------------------------------- Duangrudee Tanramluk, Ph.D. Institute of Molecular Biosciences, Mahidol University Puttamonthon 4 Rd., Salaya, Nakhon Pathom 73170 THAILAND http://manoraa.org
