Notation Schemes

To be able to efficiently handle various carbohydrate notations, MonosaccharideDB has implemented a "Notation Scheme" concept. Each alias name, regardless if it denotes a monosaccharide, a substituent, an aglycon or any other component, is assigned to a notation scheme. For each component, there is exactly one primary alias name defined for each scheme (or, strictly speaking, none or one primary alias, as some components are not defined in all notations). In addition, there might be several secondary alias names available.

Currently, the MonosaccharideDB web interface supports the following notation schemes:


MonosaccharideDB

MonosaccharideDB's internal notation format. Basetype and substituent names are the same as in GlycoCT, with the exception that "anhydro" and "lactone" modifications are included in the basetype here, while they are defined as substituents in GlycoCT. As most glycobiologist and also most carbohydrate databases consider a monosaccharide that contains substituents as one residue, they are defined in this way in MonosaccharideDB as well.


CarbBank

The CarbBank notation is based on the IUPAC extended notation. It is used by the Complex Carbohydrate Structure Database (CCSD), which is better known by the name of its query software "carbbank". CarbBank style notation forms the basis of several other notations, such as the Glycosciences.de scheme.


Glycosciences.de

The Notation used in the Glycosciences.de web portal. It is based on the CarbBank notation.


GlycoCT

The nomenclature that is used by EUROCarbDB. For more information see www.eurocarbdb.org/recommendations/encoding/.


Protein Data Bank (PDB)

The 3-letter residue names as used by the Protein Data Bank (PDB). Unlike most of the other notations, these names cannot be generated automatically by conversion routines but have to be assigned manually by the database administrators. Some PDB residue names that encode carbohydrate residues define disaccharides or oligosaccharides. These are not implemented in MonosaccharideDB, as the scope of this database is on monosaccharide residues.


Bacterial Carbohydrate Structure Database (BCSDB)

The notation used by the Russian BCSDB. For more information on this notation, see the description on the BCSDB homepage.


Consortium for Functional Glycomics LinearCode (CFG)

The LinearCode notation used by the US Consortium for Functional Glycomics (CFG).


AMBER GLYCAM

Two-letter residue names used within the AMBER GLYCAM forcefield. For more information, see Carbohydrate Naming Convention in Glycam.

Note (1): Monosaccharide alias names in GLYCAM notation also encode linkage positions (in the first character of a three-letter-code residue name). These depend on the context of a residue within an oligosaccharide and thus are no monosaccharide properties. GLYCAM names stored in MonosaccharideDB refer to a terminal residue. The first character might have to be adjusted according to the specific context of a residue, i.e. in case other residues linked are to the given one.

Note (2): The GLYCAM notation is not yet supported by the notation parsing routines, i.e. GLYCAM alias names can be created, but not be read yet.