GLYCAM-Web | Utilities for molecular modeling of carbohydrates

What glycans bind to my protein?

If you have access to a crystal structure of a carbohydrate bound to a protein, this tool will use that single co-complex as a basis for predicting which other similar glycans are also likely to bind to the same protein.

Overview

This tool uses carbohydrate grafting [1,2] to build 3D structures of glycan-protein structures. The tool can predict which glycans among a group that all share a common motif are likely to bind to a given protein known to recognize that motif. A motif is typically two or three monosaccharides.


Requirements

A set of 3D coordinates for a protein complexed with a carbohydrate ligand. Coordinates may be found and downloaded from the Protein Data Bank (PDB) or from GlyFinder.

For example, test this tool using the PDB file 2iho.pdb, which contains a trisaccharide bound to a lectin from Marasmius oreades [1,3].


Actions

Specificity Prediction
Predict the glycans that bind to a protein with a known 3D co-structure.


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