JAAG: a JSON input file Assembler for AlphaFold 3, OpenDDE, Protenix, OpenFold 3, Chai-1, and Boltz with Glycan integration

JAAG is a web-based tool designed to assemble input files for standalone AlphaFold 3, OpenDDE, Protenix, OpenFold 3, Chai-1, and Boltz.

How to add glycans?
  1. Protein: 'Detect sequons' or add 'Glycosylation sites'
  2. Ligand: 'Glycan' is the default input type
Where to find GlycoCT?
  1. Draw a glycan in a popup SugarDrawer
  2. External glycan database: GlyGen, GlyTouCan, GlyConnect, etc
Reference
  1. Please refer to this paper to properly interpret the AlphaFold 3 glycan-related models:
    2. Huang, C., Kannan, N., & Moremen, K. W. (2025). Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations. Glycobiology, 35(10), cwaf048
  2. If you use JAAG in your research, please cite:
    3. Huang, C., & Moremen, K. W. (2025). JAAG: a JSON input file Assembler for AlphaFold 3 with Glycan integration. bioRxiv
  3. JAAG source code and detailed guide can be found on JAAG GitHub and AlphaFold 3 GitHub
Funding
  • This project is supported by U.S. National Science Foundation BioFoundry: Glycoscience Research, Education and Training and University of Georgia
Basic Information
Allows letters, numbers, hyphens, and underscores
AlphaFold 3 dialect, version 1–4
v4: Adds descriptions for chains
v3: Adds userCCD path
v2: Adds external MSA/templates
v1: Basic format
Comma-separated seeds (1-4294967295 each)
Sequences

Click the buttons above to add sequences

Use hyphen in new userCCD code to avoid parsing errors
Path to CCD mmCIF file
Active userCCDs:
No manual userCCD added yet.
AlphaFold 3 JSON Output
Add a sequence to create AlphaFold 3 JSON
Ready to generate JSON
Share links embed the input data. Compression is not encryption.