JAAG — glycan modelling for AlphaFold 3

Chin Huang, a graduate student in Dr. Kelley Moremen’s BioF:GREAT laboratory, has developed a web-based tool that helps glycan modeling by Alphafold 3.

What JAAG does

AlphaFold 3 can accurately model glycans with proper stereochemistry only when using the BAP+CCD syntax, but manually creating these inputs is tedious and error-prone. To streamline the process, JAAG—a lightweight, user-friendly web tool—automates the conversion of glycans drawn by users into BAP+CCD syntax. This makes it easier for scientists to model glycoproteins and glycan–protein interactions, helping even AlphaFold 3 beginners generate reliable, stereochemically valid structures effortlessly.

Use JAAG Manuscript Tutorial (PDF) Animated tutorial
Chin Huang, developer of JAAG
Chin Huang, graduate student in the Moremen laboratory and developer of JAAG.

Workflow

JAAG workflow figure
JAAG workflow — figure 1
JAAG workflow figure
JAAG workflow — figure 2
Questions. For help with JAAG inputs or interpretation of the generated structures, contact the BioF:GREAT team.