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JAAG – 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.

  • 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

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