hi Rui
RCSB run a facility called Ligand-Expo (formerly Ligand-Depot.) You
sketch a fragment of a ligand and it runs a graph search on the
ligands in the PDB.
http://ligand-expo.rcsb.org/
chiralities are not specified so it is perfect for your sugar query
best wishes
Pete
Quoting rui <ruis...@gmail.com>:
Dear all,
I want to pull out the sugar binding proteins from the pdb, however, there
are so many different names for the ligand ( GAL, GLC, RIP... ) and it's not
easy to get a complete list. If I want to pull out some fragments based on a
specific geometry ( for instance, the glucose has C1 C2 C3 C4 C5 C6, and I
want to use the geometry for instance, O5,C1, O1, C2 and O2 to pull out all
the ligands that contains this kind of geometry. Is there any
straightforward way to do it?
Thanks a lot.
