Glycoconjugate Data Bank:Structures -: an annotated glycan structure database and N-glycan primary structure verification service
Glycoconjugate Data Bank:Structures -: an annotated glycan structure database and N-glycan primary structure verification service
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DOI：
10.1093/nar/gkm833
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发表时间：
2008-01-01
影响因子：
14.9
通讯作者：
Nishimura, Shin-Ichiro
中科院分区：
文献类型：
--
作者：
Nakahara, Taku;Hashimoto, Ryo;Nishimura, Shin-Ichiro
糖生物学作为后基因组时代的前沿领域受到了公众的关注。有关聚糖的结构信息多年来一直在蛋白质数据库 (PDB) 中积累。然而，人们已经认识到 PDB 中存在许多有问题的聚糖模型。显然需要一种验证聚糖 3D 结构一级结构的工具，但目前还没有这样的公开工具。糖复合物数据库：结构（GDB:Structures，http://www.glustructurals.jp）是一个带注释的聚糖结构数据库，还提供 N-聚糖一级结构（或糖型）验证服务。所有聚糖 3D 结构均由名为“getCARBO”的内部程序检测和注释。当 getCARBO 在查询坐标中检测到 N-聚糖时，会将聚糖的一级结构与聚糖一级结构数据库 (KEGG GLYCAN) 中最相似的条目进行比较，如果观察到不匹配的子结构，则会指示出来。 getCARBO 的结果存储并呈现在 GDB：结构中。
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.