pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files

Background: Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of glycans is a prerequisite for a complete understanding of their biological functions. The largest source of biomolecular 3D structures is the Protein Data Bank. However, about 30% of all 1663 PDB entries (version September 2003) containing carbohydrates comprise errors in glycan description. Unfortunately, no software is currently available which aligns the 3D information with the reported assignments. It is the aim of this work to fill this gap. Results: The pdb-care program http://www.glycosciences.de/tools/pdb-care/ is able to identify and assign carbohydrate structures using only atom types and their 3D atom coordinates given in PDBfiles. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compa...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Thomas Lütteke, Claus-Wilhelm von der Lieth
• Keywords: BMCBI 2004, Fundamental Biological Processes, Pathological Situations, PDB Entries