glycans ( carbohydrate chains ) are one of the major classes of biological molecules , like nucleic acids and proteins .
there is a substantial amount of structural information about glycan 3d structures in the protein data bank ( pdb ) ( 1 ) , and this is the major resource in the structural biology of glycans .
there are two major classes of modified glycans , namely n - glycans ( asparagine - linked glycans ) and o - glycans ( serine or threonine - linked glycans ) .
the accuracy of the glycan structures in the pdb has been in question for years .
it was reported that there are some hundreds of asparagine - linked n - acetylglucosamines with inaccurate anomeric forms ( 2,3 ) .
furthermore , 30% of saccharide units in the pdb contain errors , mainly in monosaccharide nomenclature ( 4 ) .
so far , there is only one web service for checking the correspondence between the structure and nomenclature of a saccharide unit in a pdb file ( 5 ) .
recently , crispin et al . ( 6 ) pointed out that glycan structures with unreported primary structure motifs were observed in the pdb .
models of glycan 3d structures built by x - ray crystallography should be supported by the glycan primary structure data derived by other methods ( nmr , hplc , mass spectrometry and so on ) .
our recent comprehensive survey revealed that 13.6% of glycans in the pdb contains substructure(s ) which are not found in the glycan primary structure database ( 7 ) , which suggested that the pdb contains a substantial number of glycans of which primary structures can not be synthesized by known biological pathways .
a tool to verify the glycan primary structures of 3d models is in urgent demand .
the glycoconjugate data bank : structures ( gdb : structures ) is a database of annotated glycan structures .
getcarbo. furthermore , n - glycans were compared with entries in the glycan primary structure database , kegg glycan ( 8) . the kegg glycan entry with the most similar structure to the pdb glycan is selected by using a glycan structure search function implemented in getcarbo , and unmatched substructure(s ) between the glycan found in the pdb and the most similar kegg glycan entry were noted graphically .
gdb : structures also provides a web service for checking glycan structures in a user - uploaded structure file by getcarbo . as far as we know , there have been no verification services for glycan primary structures . the widely used site , pdb - care ( 5 ) , a verification service for nomenclature of a saccharide unit , does not have a functionality to verify a glycan primary structure .
gdb : structures provides functionality not only of verifying monosaccharide structures , but also that of glycan primary structures , and will compensate for the lack of tools for modeling biologically meaningful glycan 3d structures .
gdb : structures is running on ruby on rails framework with lighttpd web server and mysql database management system .
all the glycans in gdb : structures are classified into three types : ligands , n - glycans and o - glycans .
users can retrieve lists of glycans by specifying the type and length of the glycans .
users can draw query glycan primary structures on the flash web interface and obtain a list of similar glycans in gdb : structures .
the contents of gdb : structures will be updated regularly , and the statistics of the current content is also presented . in each glycan information page , the primary structure of the glycan and annotations for the glycan and monosaccharide units are presented . in the case of n - glycan ,
the most similar kegg glycan entry is also presented . for each monosaccharide unit , the identifier in the pdb , iupac nomenclature ( 9 ) , common name , anomeric form and chair conformation are presented .
the kegg glycan entries are linked to the original data in kegg ( 10 ) .
the three - letter - identifiers of each monosaccharide unit are linked to het - pdb navi ( 11 ) .
each of the pdb entries in gdb : structures is mutually linked with that in the pdbj ( 1 ) .
users can interactively browse the 3d structural model of the pdb entry by using a jmol applet ( www.jmol.org ) .
users can upload their structure file ( pdb format ) to gdb : structures to annotate glycan structure(s ) in the file by getcarbo .
the results of the annotation will be sent back to the users by email , normally within a few minutes after uploading .
the html file presents the results in the same format as the glycan information page of gdb : structures . in the case of n - glycan ,
the most similar kegg glycan entry is presented , and unmatched substructures are noted by red question marks .
o - glycans are not checked in gdb : structures , because studies on the structures of ( especially , non - mammalian ) o - glycans have not reached the critical mass to perform database searches compared to those on n - glycans , of which primary structures and biosynthetic pathways are well known . 

an html file containing results of glycan annotation is sent back to the user who submitted a structure file ( pdb format ) .
the glycan structure detected in the user - uploaded file is shown in the  structure record and the most similar kegg glycan entry is shown in the  kegg analogue record .
unmatched substructures ( glycoside bonds between mannose residues ) are indicated by red question marks .
an html file containing results of glycan annotation is sent back to the user who submitted a structure file ( pdb format ) .
the glycan structure detected in the user - uploaded file is shown in the  structure record and the most similar kegg glycan entry is shown in the  kegg analogue record .
unmatched substructures ( glycoside bonds between mannose residues ) are indicated by red question marks .
gdb : structures is not only an annotated glycan structure database , but also a web service for verifying the primary structures of glycan 3d structures , which is in high demand by structural biologists ( 12 ) .
this database will help users to determine the characteristics of the glycan structures of their interests and also allow structural biologists to verify their determined glycan structures .
our n - glycan checking process is not always valid and is limited due to the nature of the reference glycan primary structure database .
if the glycan primary structure is not found in the reference database , the annotation by getcarbo will point out unmatched substructures on a query glycan structure , even though the 3d structure is built on x - ray diffraction data fine enough to assign unreported motifs .
: structures will be publicly available following the establishment of an international consensus on the glycan description format ( 1315 ) .
 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 . 
INTRODUCTION
STRUCTURE AND CONTENT OF GDB:SRUCTURES
GLYCAN STRUCTURE ANNOTATION SERVICE
CONCLUSION AND FUTURE PERSPECTIVES