GLYCAM-Web | Utilities for molecular modeling of carbohydrates

Search for glycans in the PDB?

Overview

Use Glycam Web to create the files you need to represent a glycan and the various shapes it is likely to assume.

Protocol

  1. First generate a condensed sequence that represents your glycan, using one of the following methods:
  2. Next, you will be asked to set options for your glycan. Any of these can be set or ignored as you see fit.
    • Select rotamers to download,
    • Set specific angles,
    • Choose whether or not to add solvation and set solvation properties.
  3. After you submit your optional settings, you will be shown a 3D visualization of your glycan in the browser.
  4. Finally, you may donwload structure files for use with other tools or software.

Output

Structure files contain the data needed to represent a glycan in a given pose. You can download a separate structure file for each pose you need, all in one pass with the Carbohydrate Builder. This data is useful as input in other software, such as VMD for 3D visualization, or other tools on Glycam Web.

Resources

For a detailed explanation of this process, as well as how to load your downloaded structure files into VMD, please visit our Scenario Documentation.
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