What are the shapes of my glycan?
Generate and display 3D structures of the expected shapes of a glycan and download files for viewing offline or for use in other modeling applications, such as for performing MD simulations with AMBER.
Overview
The tools below help you to assemble or select a glycan, which is then automatically energy minimized with the GLYCAM force field [1] to generate one or more 3D models. The file formats available for download include PDB (coordinates), as well as AMBER (topology and coordinates). The beta-test Carbohydrate Builder does not currently provide files for MD simulation.
Requirements
- A familiarity with carbohydrate nomenclature.
Actions
Assemble a glycan by connecting monosaccharides. This is the legacy tool.
Assemble a glycan by connecting monosaccharides. This new tool is still in development.
Assemble a glycosaminoglycan by connecting monosaccharides.
Select a glycan from libraries of common structures.
Type-in or copy-paste a glycan sequence in GLYCAM text format.
Set a repeating unit, and optionally add a head and/or tail.
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