Main Help Predict NMR Chemical Shifts Component Analysis Determine Glycan Structure

CASPER - Determine Glycan Structure

Determine Glycan Structure

Project ?
If you want to use structures and shifts from a CCPN
project specify the file name here. The project should
be tarred and gzipped (.tar.gz).
Title ?
In this field you type the title of the project or the name of the glycan.
Source ?
This is the literature source of the structure.
Choose aglycone: ?
If you want to include an algycone at the reducing end,
choose one from the dropdown menu. This one will automatically
be added to the anomeric position of residue 1) upon pressing
"Start Simulation".
?
Residues are selected from the pull-down menus.
Some residues are only available from the first menu.
After that the possible linkage positions are checked.
The available linkage positions depend on the kind of
residue.
The types of residues and the linkage positions are
obtained from sugar (component) analysis and
methylation (linkage) analysis.
If the linkage of a residue is unknown select the *
column. This checks all possible linkage positions
and this will also make it possible to take them
all into account when determining the structure.
Unchecking the * column will erase the linkage
positions of that residue.
2)
3)
4)
5)
6)
7)
8)
9)
10)
Chemical shifts 1D 2D ?
Select if you want to input 1-dimensional and/or 2-dimensional NMR data.
1-dimensional data is 13C and/or 1H chemical shifts.
2-dimensional data is HSQC/HETCOR chemical shifts.
13C 1H
C chemical shifts


Correct by subtracting ppm
H chemical shifts


Correct by subtracting ppm ?
If there is a known systematic error in the chemical shifts a correction can be applied.
Number of chemical shifts -
Anticipated: Actual: Number of chemical shifts -
Anticipated: Actual:
HSQC/HETCOR TOCSY
C-H chemical shifts

H-H correlations from anomers

Number of chemical shift pairs
HMBC H2BC
C-H correlations from anomers

C-H correlations from anomers

Number of chemical shift pairs
Minimum number of coupling constants of different magnitudes ?
If the numbers of coupling constants within different magnitudes are
known they can be provided here. The numbers given are the minimum
numbers and therefore it is not essential to fill in these fields
but it can improve the results.
small medium large
3JHH (<2 Hz) (2-7 Hz) (>7 Hz)
1JCH (<169 Hz) (>169 Hz)
Show/hide advanced options

Substituent Residue Position
1)
3)
5)
7)
9)
11)
13)
15)
17)
19)
21)
23)
25)
Linking to Position
Residue 1:
Residue 2:
Residue 3:
Residue 4:
Residue 5:
Residue 6:
Residue 7:
Residue 8:
Residue 9:
Residue 10:
Biological rules:
N Glycan
O Glycan
WecA Repeating Unit
Shigella flexneri
Haemophilus influenza

Free anomer in reducing end
Uncertain absolute configurations
Uncertain ring size (pyranose/furanose)

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