JAAG: a JSON input file Assembler for AlphaFold 3 with Glycan integration
JAAG is a web-based tool designed to facilitate the assembly of input JSON files for standalone AlphaFold 3.
How to add glycans?
- Protein: 'Detect sequons' or add 'Glycosylation sites'
- Ligand: 'Glycan' is the default input type
Where to find GlycoCT?
- Draw a glycan in a popup SugarDrawer
- External glycan database: GlyGen, GlyTouCan, GlyConnect, etc
Reference
- Please refer to this paper to properly interpret the AlphaFold 3 glycan-related models: Huang, C., Kannan, N., & Moremen, K. W. (2025). Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations. Glycobiology, 35(10), cwaf048
- If you use JAAG in your research, please cite: Huang, C., & Moremen, K. W. (2025). JAAG: a JSON input file Assembler for AlphaFold 3 with Glycan integration. bioRxiv 2025.10.08.681238
- 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
Getting Started: Fill in the basic information below, then add your sequences to generate a complete AlphaFold 3 input JSON file.
Basic Information
Allows letters, numbers, hyphens, and underscores
v4: Adds descriptions for chains
v3: Adds userCCD path
v2: Adds external MSA/templates
v1: Basic format
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.
JSON Output
Click "Generate" to create AlphaFold3 JSON