JAAG is a comprehensive web-based tool for generating AlphaFold 3 input JSON files with advanced glycan structure support and integrated SugarDrawer functionality. Web tool link: https://biofgreat.org/JAAG/

• Complete AF3 v4 Support: Full implementation of AlphaFold 3 v4 input format specification
• Multi-sequence Modeling: Support for protein, ligand, RNA, and DNA sequences in complex assemblies
• Real-time JSON Generation: Automatic JSON updates as inputs change with live validation
• Sequence Multimer: Automatic appending of iterated alphabets after the user-defined chain ID
• Advanced Configuration: Model seeds generator (single/multiple), MSA files, templates, custom CCDs
• AF 3 Input Full Guide: https://github.com/google-deepmind/alphafold3/blob/main/docs/input.md

• Integrated SugarDrawer: Built-in glycan drawing interface with popup modal support
• GlycoCT Processing: Full GlycoCT format parsing and conversion to bondedAtomPairs + CCD codes
• Substituent Handling: Support for glycan sulfation, phosphorylation, acetylation and methylation
• Glycoinformatics Database Lookup: Look up glycan information from GlyGen and GlyTouCan

• Sequon Detection: Detection of N-linked glycosylation sequons (N-X-S/T)
• Glycosylation Sites: Manual addition of custom glycosylation sites

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

1. Basic Setup: Enter job name
2. Add Sequences: Use the sequence buttons to add proteins, ligands, RNA, or DNA
3. Draw Glycans: Click the pencil icon to open SugarDrawer for glycan structure drawing
   Alternatives: Copy and paste GlycoCT from a glycoinformatics database
4. Generate JSON: JSON is automatically generated in real-time
5. Export: Copy or download your complete AlphaFold 3 input file

1. Download: Download or clone this repo to your local machine
2. Install Dependencies: Install Node.js then in SugarDrawer directory, run:

   npm install
   

   npm run build
   

   SugarDrawer will be built and the GAG templates will be patched
3. Open the Tool: Launch index.html in a modern web browser

1. Job Name: b3gnt2_dimer
2. Add protein sequence with chain ID BTHREEGNTTWO
   Note: only alphabets are allowed
3. Enter sequence: MSVGRRRIKL...
   Alternatives: enter UniProt ID Q9NY97 to fetch the sequence
4. Toggle Count to 2 for dimer
5. Complete JSON is ready for AlphaFold 3

1. Add protein sequence
2. Enable "Detect sequons" to detect N-glycosylation sites
   Alternatives: manually add glycosylation sites
3. Draw glycan structure using SugarDrawer and export
   Alternative 1: select glycan from templates
   Alternative 2: copy and paste GlycoCT from glycoinformatics database
4. CCDs and bondedAtomPairs are automatically generated
5. Complete JSON is ready for AlphaFold 3

1. Add protein sequence
2. Add ligand sequence
3. Draw glycan structure using SugarDrawer and export
   Alternatives: copy and paste GlycoCT from glycoinformatics database
4. Define custom bondedAtomPairs if needed (optional)
5. Complete JSON is ready for AlphaFold 3

1. Add protein sequence
2. Add ligand sequence
3. Add CCD codes or SMILES Note: only one ligand input method can exist in a JSON file
4. Define custom bondedAtomPairs if needed (optional)
   Note 1: bondedAtomPairs is only available for CCDs
   Note 2: when linking multiple CCDs into a larger molecule, it is recommended to define them within the same chain ID
   Note 3: Atom names in each CCD are available from PDBeChem or RCSB PDB
5. Complete JSON is ready for AlphaFold 3

• Validation Required: Always validate generated JSON before submission to AlphaFold 3
• Sequence Limits: Be aware of AlphaFold 3 sequence length limitations (around 5000 tokens)
• Database Availability: External database lookups depend on server availability
• Privacy: No data is sent to servers controlled by this project. When using glycan lookup features, the app makes direct client-side requests to third-party APIs (e.g., GlyGen, GlyTouCan).

This tool builds upon excellent work from the scientific community and open-source projects:

• SugarDrawer: The Noguchi Institute (Apache-2.0)

  • License: https://www.apache.org/licenses/LICENSE-2.0
  • GitLab: https://gitlab.com/glycoinfo/sugardrawer

• SugarSketcher: The Noguchi Institute (Apache-2.0)

  • License: https://www.apache.org/licenses/LICENSE-2.0
  • GitLab: https://gitlab.com/glycoinfo/sugardrawer/SugarSketcher2.git

• Bootstrap 5: Frontend framework (MIT)

  • License: https://github.com/twbs/bootstrap/blob/main/LICENSE

• Font Awesome: Icon library (Font Awesome Free License)

  • License: https://fontawesome.com/license/free

• UniProt
• GlyGen
• GlyTouCan
• RCSB PDB
• PDBeChem

This project is supported by:

• U.S. National Science Foundation BioFoundry: Glycoscience Research, Education and Training
• University of Georgia

This project is licensed under the Apache License, Version 2.0. See LICENSE for details.

If you use JAAG in your research, please cite:

• JAAG:

@article{Huang2025,
  author  = {Huang, Chin and Moremen, Kelley W.},
  journal = {TBD},
  title   = {JAAG: a JSON input file Assembler for AlphaFold 3 with Glycan integration},
  year    = {2025},
  volume  = {TBD},
  doi     = {TBD}
}

• AlphaFold 3:

@article{Abramson2024,
  author  = {Abramson, Josh and Adler, Jonas and Dunger, Jack and Evans, Richard and Green, Tim and Pritzel, Alexander and Ronneberger, Olaf and Willmore, Lindsay and Ballard, Andrew J. and Bambrick, Joshua and Bodenstein, Sebastian W. and Evans, David A. and Hung, Chia-Chun and O’Neill, Michael and Reiman, David and Tunyasuvunakool, Kathryn and Wu, Zachary and Žemgulytė, Akvilė and Arvaniti, Eirini and Beattie, Charles and Bertolli, Ottavia and Bridgland, Alex and Cherepanov, Alexey and Congreve, Miles and Cowen-Rivers, Alexander I. and Cowie, Andrew and Figurnov, Michael and Fuchs, Fabian B. and Gladman, Hannah and Jain, Rishub and Khan, Yousuf A. and Low, Caroline M. R. and Perlin, Kuba and Potapenko, Anna and Savy, Pascal and Singh, Sukhdeep and Stecula, Adrian and Thillaisundaram, Ashok and Tong, Catherine and Yakneen, Sergei and Zhong, Ellen D. and Zielinski, Michal and Žídek, Augustin and Bapst, Victor and Kohli, Pushmeet and Jaderberg, Max and Hassabis, Demis and Jumper, John M.},
  journal = {Nature},
  title   = {Accurate structure prediction of biomolecular interactions with AlphaFold 3},
  year    = {2024},
  volume  = {630},
  number  = {8016},
  pages   = {493–500},
  doi     = {10.1038/s41586-024-07487-w}
}