JAAG (JSON input file Assembler for AlphaFold 3 with Glycan integration)

JAAG streamlines the creation of JSON input files for AlphaFold 3 simulations involving glycans and glycan-macromolecule interactions.

Key Features:

• Glycan stereochemistry preservation: Monosaccharides are specified as Chemical Component Dictionary (CCD) entries and connected using bondedAtomPairs (BAP) syntax to achieve plausible glycan stereochemistry.
• Complex glycan modeling: Handles the diversity of monosaccharides, linkages, branching, and structural complexity in glycan structures.
• AlphaFold 3 integration: Generates JSON input files for modeling proteins, post-translational modifications, ligands, and glycans in standalone AlphaFold 3.

Scientific Applications:

• Glycan structure prediction: Facilitates modeling of glycans with preserved stereochemistry in AlphaFold 3.
• Glycan-macromolecule interaction modeling: Enables simulation of interactions between glycans and other macromolecules in AlphaFold 3.
• Post-translational modification analysis: Supports modeling of glycosylation as a post-translational modification on proteins.

Methodology:

JAAG assembles JSON input files by specifying monosaccharides as Chemical Component Dictionary (CCD) entries and connecting them using bondedAtomPairs (BAP) syntax.