There are a number of useful tools at glycoscience.de http://www.dkfz.de/spec/glycosciences.de/tools/index.php
Unfortunately, none of them may be **exactly** what you are looking for... pdb2linucs - extracts carbohydrate information from pdb files (definitely not a trivial task considering the lack of standard nomenclaure for carbohydrates) and displays it using either the LINUCS code or the IUPAC notation. GlyVicinity - is quite a powerful program for PDB-wide analysis of protein-carbohydrate interaction geometries. It works on a weekly updated database generated by ploughing the pdb with pdb2linucs. All the best, Tim PhD Student Medizinische Hochschule Hannover Zelluläre Chemie, OE 4330 Zentrum Biochemie Carl-Neubergstr. 1 30625 Hannover -----Original Message----- From: CCP4 bulletin board on behalf of rui Sent: Fri 17.04.2009 05:13 To: CCP4BB@JISCMAIL.AC.UK Subject: [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 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.
