Points to note about GlycoCT

  1. Underdetermined capping unit
  2. Selection of residues connecting ambiguous antenna residues
  3. Change of substituent type
  4. Available substituents in GlycoCT

1. Underdetermined capping unit

GlyTouCan - G02402FF

incorrect GlycoCT

Point: SubtreeLinkageID1:u(-1+1)u

RES
1b:b-dglc-HEX-1:5
2s:n-acetyl
3b:b-dglc-HEX-1:5
4s:n-acetyl
5b:b-dman-HEX-1:5
6b:a-dman-HEX-1:5
7b:a-dman-HEX-1:5
LIN
1:1d(2+1)2n
2:1o(4+1)3d
3:3d(2+1)4n
4:3o(4+1)5d
5:5o(3+1)6d
6:5o(6+1)7d
UND
UND1:100.0:100.0
ParentIDs:1|3|5|6|7
SubtreeLinkageID1:u(-1+1)u
RES
8b:x-dman-HEX-1:5

correct GlycoCT

Point: SubtreeLinkageID1:o(-1+1)d

RES
1b:b-dglc-HEX-1:5
2s:n-acetyl
3b:b-dglc-HEX-1:5
4s:n-acetyl
5b:b-dman-HEX-1:5
6b:a-dman-HEX-1:5
7b:a-dman-HEX-1:5
LIN
1:1d(2+1)2n
2:1o(4+1)3d
3:3d(2+1)4n
4:3o(4+1)5d
5:5o(3+1)6d
6:5o(6+1)7d
UND
UND1:100.0:100.0
ParentIDs:1|3|5|6|7
SubtreeLinkageID1:o(-1+1)d
RES
8b:x-dman-HEX-1:5

2. Selection of residues connecting ambiguous antenna residues

  1. Build glycan with a bracket using GlycoWorkbench (or GlycanBuilder) bracket1
  2. Export to GlycoCT format bracket2
  3. Find residues related to ambiguous antenna and their ID numbers in the GlycoCT bracket3 1
  4. Change the ID numbers specified at “ParentIDs” in the GlycoCT to select parent residues of ambiguous antenna
    • Also need to change the connecting type in “SubtreeLinkageID” bracket4-1 1 bracket4-2 1

3. Change of substituent type

  1. Build glycan with a substituent using GlycoWorkbench (or GlycanBuilder)
    • The substituent must be able to convert to GlycoCT (e.g. phosphate) modSubstituent1
  2. Export to GlycoCT format modSubstituent2
  3. Find the substituent residue in the GlycoCT
  4. Change the substituent name to the other one which you want to add modSubstituent4-1 1 modSubstituent4-2 1

4. Available substituents in GlycoCT

substituents

Available substituents in GlycoCT