Glycoconjugate Data Bank:Structures an annotated glycan structure database and N-glycan primary structure verification service

Abstract

Glycobiology has been brought to public attention as a frontier in the post-genomic era. Structural information about glycans has been accumulating in the Protein Data Bank (PDB) for years. It has been recognized, however, that there are many questionable glycan models in the PDB. A tool for verifying the primary structures of glycan 3D structures is evidently required, yet there have been no such publicly available tools. The Glycoconjugate Data Bank:Structures (GDB:Structures, http://www.glycostructures.jp ) is an annotated glycan structure database, which also provides an N -glycan primary structure (or glycoform) verification service. All the glycan 3D structures are detected and annotated by an in-house program named ‘getCARBO’. When an N -glycan is detected in a query coordinate by getCARBO, the primary structure of the glycan is compared with the most similar entry in the glycan primary structure database (KEGG GLYCAN), and unmatched substructure(s) are indicated if observed. The results of getCARBO are stored and presented in GDB:Structures.