Glycoconjugate Data Bank: Structures--an annotated glycan structure database and N-glycan primary structure verification service.
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.
Nakahara
Taku
T
Laboratory of Advanced Chemical Biology, Graduate School of Advanced Life Science, Frontier Research Center for the Post-Genomic Science and Technology, Hokkaido University, Sapporo, Japan.
Hashimoto
Ryo
R
Nakagawa
Hiroaki
H
Monde
Kenji
K
Miura
Nobuaki
N
Nishimura
Shin-Ichiro
S
D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D016208:Databases, Factual; D030562:Databases, Protein; D006001:Glycoconjugates / Q000737:chemistry*; D006023:Glycoproteins / Q000737:chemistry; D020407:Internet; D011134:Polysaccharides / Q000737:chemistry*; D014584:User-Computer Interface
D006001:Glycoconjugates; D006023:Glycoproteins; D011134:Polysaccharides