Help kf: rate-limiting turn over rate
Km: dissociation constant of the oligosaccharide-enzyme complex
Kmd: dissociation constant of the nucleotide sugar donor-enzyme complex
Kmn: dissociation of the nucleotide by product-enzyme complex
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Linear Code


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5. Check prediction method:
  •  Forward Prediction
  •  Forward Prediction with glycoprofile
  •  Backward Prediction
  •  Backward Prediction with initial glycans

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    *This page can be available after GPP program was excuted.

    Description

    You can compare predicted glycans with ones from your csv file. The glycans represented by Linear Code supports one monosaccharide uncertainty '*' and linkage or anomer uncertainty '?'. For instance, "*Ab?GNb?ANa;S" has one unknown monosaccharide and uncertain linkage between GlcNAc(GN) and GalNAc(AN). Furthermore, you should set 'Glycan Type' to assign where the glycan is attributed to (e.g. N, O, L).

    CSV file with Linear Code and Glycan Type is required to compare.
    Sample Template for N-type glycans and O-type glycans of Mouse ES cells from Nairn et al.
    This page searches enzyme specificity data from GlycoSimDB.
    1. Click the 'Species' tab to specify one species, then enzyme specificities data are displayed by either 'Table' style or 'List' style.
    2. We pick up these data and use them in 'Checked List' page.
    Some data colored orange means ''
    Species: 
    Enzyme Name: 
    5. Check prediction method:
    •  Forward Prediction
    This page shows an example of mucin O-type glycan pathway.
    1. You can edit these parameters (i.e. Enzyme name, Class, Type, etc.) by changing these variables, and make sure all variables are correctly validated by cheking the background color is green.
    2. Enzyme specificities data can be displayed by either a table or a list. If all data are corrected, then we need to specifiy initial glycans.
    3. To setting initial glycans, we need to attribute index, LinearCode Representaion, number of monosaccharides, Glycan type into the textarea shown below (e.g. 1,;S/T,0,O)
    4. Set max monosaccharide size not to predict too much reactions.
    5. Push button to predict.
    4. Check prediction method:
    •  Forward Prediction
    • title

    Glycans:

    Enzymes:

    Donors:

    Parameters:

    Reactions:

    Reactions detail:

    Functions:

    1. Setting Time-Course simulation duration time and step number.

    2. Click to run simulation.
    Individual plot
    Parameters plot
    Glycan ratio
    If you want to execute the parameter estimation program, you have to login or signup to the GlycoSim in advance.
    Description: We can estimate parameters such as kf, Km, Kmd, Et of each reactions. To do that, we need to select which parameter should be estimated, and experimental data of glycan species. Model detail
    1. Use checkbox to decide estimation parameters.
    Filter by:
    2. Set experimental data
    Estimation by:
    3. setting estimation algorithm configuration.
    Method:
    Sensitivity Analysis calculates each species sensitivities of each target items. 'Target' means which kinds of objects should change. For example, the target 'parameter' changes the value itself at the rate of 1.01. 'Metric' means
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