Nucleic Acids Research Advance Access originally published online on October 11, 2007
Nucleic Acids Research 2008 36(Database issue):D368-D371; doi:10.1093/nar/gkm833
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Nucleic Acids Research, 2008, Vol. 36, Database issue D368-D371
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
Glycoconjugate Data Bank:Structures—an annotated glycan structure database and N-glycan primary structure verification service
1Laboratory of Advanced Chemical Biology, 2Laboratory of Glyco-Fine Chemistry, 3Sun Microsystems Laboratory of Computational Molecular Life Science, Graduate School of Advanced Life Science, Frontier Research Center for the Post-Genomic Science and Technology, Hokkaido University, Sapporo 001-0021 and 4Science & Technology Systems Inc. Tokyo, 150-0002, Japan
* To whom correspondence should be addressed. Tel: +81 11 706 9043; Fax: +81 11 706 9042; Email: shin{at}glyco.sci.hokudai.ac.jp
Received August 13, 2007. Revised September 20, 2007. Accepted September 21, 2007.
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.