Dear AlphaFold 3 Development Team and Community,

First of all, thank you again for making AF3 publicly accessible and for fostering such an insightful discussion space.

We are excited to share JAAG, JSON input file Assembler for AlphaFold 3 with Glycan integration, a lightweight web-based GUI tool that generates AF3 input .json files with integrated glycan functionality.

We previously reported that AF3 generates improved stereochemistry on glycans when using bondedAtomPairs + CCD syntax. However, manually composing the .json files can be tedious and error-prone. JAAG automates this process, generating the correct syntax for glycans along with all other AF3 configuration fields. It is designed to help researchers easily build glycoprotein systems or glycan-protein complexes without manually editing JSON files.

Compatibility:

• Fully compatible with standalone AF3
• Not compatible with the AlphaFold 3 public server

Web app: https://biofgreat.org/JAAG

No user data or JSON content is stored or processed on our server.

Open-source code: https://github.com/chinchc/JAAG
Preprint: https://www.biorxiv.org/content/10.1101/2025.10.08.681238v1
Reference on interpreting AF3 glyco-related models: https://doi.org/10.1093/glycob/cwaf048

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