Three-Dimensional Structure Database of Natural Metabolites (3DMET): A Novel Database of Curated 3D Structures
Three-Dimensional Structure Database of Natural Metabolites (3DMET): A Novel Database of Curated 3D Structures
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DOI：
10.1021/ci300309k
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发表时间：
2013-03-01
影响因子：
5.6
通讯作者：
Kondo, Kazumi
中科院分区：
文献类型：
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作者：
Maeda, Miki H.;Kondo, Kazumi
开发了一个名为3DMET的天然代谢物三维结构数据库。在从2D到3D的结构转换过程中，我们发现许多结构在手性原子和键上发生了错误的转换。对几种流行的转换器进行了转换精度测试。为了验证，还测试了三个规范字符串。没有一种方法能令人满意地涵盖天然产物的所有结构。错误转换的结构必须手动更正。然而，即使在人工管理之后，也观察到了不可忽略的数量的错误，因此开发了一个自我检查系统，并将其引入我们的工作流程。因此，我们的3DMET数据库中的3D结构分两个步骤进行评估：自动和手动。当前版本包括KEGG复合集合[http://www.genome.jp/kegg/compound/]]的大多数天然产品，并且可以通过字符串、值范围和子结构进行搜索。3DMET可通过http://www.3dmet.dna.affrc.go.jp/，访问，该网站也有详细的手册。
A database of 3D structures of natural metabolites has been developed called 3DMET. During the process of structure conversion from 2D to 3D, we found many structures were misconverted at chiral atoms and bonds. Several popular converters were tested in regard to their conversion accuracy. For verification, three canonical strings were also tested. No procedure could satisfactorily cover all the structures of the natural products. The misconverted structures had to be corrected manually. However, a nonnegligible number of mistakes were also observed even after manual curation, so a self-checking system was developed and introduced to our work flow. Thus, the 3D structures in our 3DMET database were evaluated in two steps: automatically and manually. The current version includes most of the natural products of the KEGG COMPOUND collection [http://www.genome.jp/kegg/compound/] and is searchable by string, value range, and substructure. 3DMET can be accessed via http://www.3dmet.dna.affrc.go.jp/, which also has detailed manuals.