The “condensed” oligosaccharide notation

Documentation in progress.  Please be patient.

The condensed oligosaccharide notation is recognized by GLYCAM-Web when building via URL or by text entry online.  It is very similar to the , but is condensed, and it is also beased on common abbreviations given in .

The condensed oligosaccharide notation is recognized by GLYCAM-Web when building via URL or by text entry online.  It is very similar to the “glycam” notation, but is condensed, and it is also beased on common abbreviations given in Table 1 on the page describing the force field residue naming convention.

The primary differences between condensed and glycam are:

  • The location of the alpha/beta indication
    • In condensed notation, this indication happens near the linkage, not at the beginning of the monosaccharide.
  • The quantity of punctuation
    • Condensed notation reduces the required number of characters.

For example,

glycam:  a-D-Glcp-(1-4)-b-L-Manp-OH
condensed:  DGlcpa1-4LManpb1-OH

Important things to note:

  • There can be no spaces in the notation.
  • The identity of the moiety at the reducing end must be specified explicitly (e.g., -OH or -OME).

For example, chitobiose would be,

DGlcpb1-4DGlcpb1-OH
Its methyl glycoside would be:
DGlcpb1-4DGlcpb1-OME

Branches are handled with square brackets. To specify an alpha, L rhamnopyranoside with DManpa1-3DManpa1- attached at the three position and DGalpb1-4DGalpb1- attached at position four, you would use:
DManpa1-3DManpa1-3[DGalpb1-4DGalpb1-4]LRhapa1-OH

In anomeric – to – anomeric likages (e.g., sucrose and trehalose), the notation is the same, but trailing linkage information is not appropriate.
Trehalose: DGlcpa1-1DGlcpa
Sucrose: DFrufb2-1DGlcpa