KCF (KEGG Chemical Function) format is the standard format used by RINGS and KEGG. An example of the KCF text for the fucosylated N-glycan core with a bisecting GlcNAc is given below.
ENTRY Fuc_Bis_N Glycan
1 fuc 12.0 7.0
2 glcnac 19.0 2.0
3 glcnac 12.0 2.0
4 man 5.0 2.0
5 man -2.0 7.0
6 glcnac -2.0 2.0
7 man -2.0 -3.0
1 1:a1 2:6
2 3:b1 2:4
3 4:b1 3:4
4 5:a1 4:6
5 6:b1 4:4
6 7:a1 4:3
There are three major sections: ENTRY, NODE and EDGE.
- The ENTRY section consists of one line
and may specify a name for the structure followed by the keyword Glycan.
- The NODE section consists of several lines. The first line contains the number of monosaccharides
or aglycon entities, and the following lines consist of the details of these entities numbered
consecutively. For each entity line, the name and x- and y-coordinates (to draw on a 2D plane)
must be specified.
- Similarly, the EDGE section consists of several lines, the first line containing
the number of bonds (usually one less than the number of NODEs), followed by the details of the
bond information. The format for the bond information is as follows:
- num <donor node#>:<anomeric configuration (a or b)><donor carbon#> <acceptor node#>:<acceptor carbon#>