Re: [ccp4bb] build fragment library from pdb based on a specific geometry

The most general solution to this problem boils down to one of graph isomorphism: http://en.wikipedia.org/wiki/Graph_isomorphism James On Apr 16, 2009, at 8:13 PM, rui wrote: Dear all, I want to pull out the sugar binding proteins from the pdb, however, there are so many different

Re: [ccp4bb] build fragment library from pdb based on a specific geometry

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

Re: [ccp4bb] build fragment library from pdb based on a specific geometry

: [ccp4bb] build fragment library from pdb based on a specific geometry 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

[ccp4bb] build fragment library from pdb based on a specific geometry

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