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# Community Tools

## JAAG – JSON input file Assembler for AlphaFold 3 (with Glycan Integration)
## JAAG: a JSON input file Assembler for AlphaFold 3 (with Glycan Integration)

JAAG is a lightweight, web-based GUI tool that helps generate AlphaFold 3 input
JSON files with integrated glycan support. It automates the creation of correct
glycan syntax (including `bondedAtomPairs` + CCD), reducing manual errors when
preparing glycoprotein or glycan–protein systems.
JAAG is a lightweight, web-based GUI tool that helps generate AlphaFold 3 input JSON files with integrated glycan support. It automates the creation of correct glycan syntax (including `bondedAtomPairs` + CCD), reducing manual errors when preparing glycoprotein or glycan–protein complexes.

* Web app: https://biofgreat.org/JAAG
* Source code: https://github.com/chinchc/JAAG
* Preprint: https://www.biorxiv.org/content/10.1101/2025.10.08.681238v1
* Reference: Chin Huang, Kelley W Moremen, Editor’s Choice JAAG: a JSON input file assembler for AlphaFold 3 with glycan integration, Glycobiology, Volume 36, Issue 1, January 2026, cwaf083, https://doi.org/10.1093/glycob/cwaf083

Note: JAAG is compatible with standalone AlphaFold 3, but not with the AlphaFold
3 server.

## Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations

We would like to share our recent work on modeling glycans (and other ligands) with AF3. We modeled and assessed major glycan classes and provided practical resources:
* Step-by-step tutorial for building ligand inputs (applicable beyond glycans)
* Ready-to-run scripts for each glycan class
* Comprehensive CCD table for all SNFG monosaccharides
* Discussion of caveats and limitations of AF3
* Full AF3 inputs/outputs openly archived on ModelArchive for reproducibility

If your AF3 ligand models appear stereochemically off, give it another try!

Reference: Chin Huang, Natarajan Kannan, Kelley W Moremen, Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations, Glycobiology, Volume 35, Issue 10, October 2025, cwaf048, https://doi.org/10.1093/glycob/cwaf048
ModelArchive: https://doi.org/10.5452/ma-af3glycan

Thanks,
Chin Huang | Moremen Lab
Ph.D. Candidate & Graduate Research Assistant
Department of Biochemistry and Molecular Biology
Complex Carbohydrate Research Center
University of Georgia