In the Japan Consortium for Glycobiology and Glycotechnology DataBase (JCGGDB) which is open to the public,
there are databases that integrate structural information of glyco-related compounds,
including JMSDB which stores structural information of such basic monosaccharides as glucose and fucose,
JIGSDB which stores more complex glycan structural information,
and a database which stores structural information of glycosides including inhibitors such as glycosyltransferase and glycosidase.
However, because glyco-related compounds stored in JCGGDB are composed of not just monosaccharides but also aglycons (e.g. steroid, phenol, flavonoid),
there have been only limited uses for glycobiologists who are accustomed to searching for structures with CFG monosaccharide symbols.
To solve this problem, we have developed GlycoChemExplore,
by which molecular structures of compounds can be searched for with chemical structural formula of aglycons as well as glycans.
(Note: GlycoChemExplore does not cover glycans in JIGSDB of which bonding positions and repetition of structures are uncertain.)
GlycoChemExplore is a search system in which molecular structures of monossacharides,
glycans and a variety of other substances that have in part glycan structures,
are made into queries and searched for.
This system enables the followings
Fig. System Structure
As of March 2013, the data extracted from the following databases are registered as search targets.
Also, data are updated on a timely basis after each of the databases is updated.
GlycoChemExplorer was developed with the support of the Integrated Database Project by the Ministry of Education, Culture, Sports, Science and Technology (MEXT).
Updating of data and improvement of functions are made with the help of the Integrated Database Program sponsored by Japan Science and Technology Agency (JST) and National Bioscience Database Center (NBDC).
MEXT integrated Database Project, web site : http://lifesciencedb.mext.go.jp/
NBDC integrated Program, web site : http://biosciencedbc.jp/en/
The Research Center for Medical Glycoscience of the National Institute of Advanced Industrial Science and Technology (AIST) makes all the efforts to provide correct and up-to-date information,
but it accepts no liability for the accuracy of information, or the correctness, completeness or usefulness of data available in this website.
How to use the system
There are four ways to use this system:
・Searching by drawing a structure (Draw a structure)
・Displaying a structure by specifying an identifier, and then editing (Draw a structure by Identifier)
・Describing a structure by text format of chemical structures file such as SMILES, MOL, SDF, CML and SYBYL, and displaying it to edit (Draw a structure by “Copy & paste”)
・Describing a structure by text format of chemical structures file, then converting it to another format (Convert)
Note: The selected function is shown by a solid line (In the example below, “Samples” is selected).
Note: MarvinSketch (ChemAxion Ltd.) is used for drawing structures, so please refer to MarvinSketch GUI for more details.
The following five search conditions can be set:
The following formats can be used for reading and converting:
MarvinSketch User's Guide:https://www.chemaxon.com/marvin/help/sketch/sketch-index.html
MarvinView User's Guide :https://www.chemaxon.com/marvin/help/view/view-index.html