Editor's Choice JAAG: a JSON input file assembler for AlphaFold 3 with glycan integration

Area of Science:

• Structural Biology
• Computational Biology
• Glycoscience

Background:

• AlphaFold 3 (AF3) models proteins, post-translational modifications, and ligands.
• Accurate glycan modeling requires specific input formats like Chemical Component Dictionary (CCD) entries and bondedAtomPairs (BAP) syntax.
• Manual creation of complex glycan structures in JSON format for AF3 is challenging and error-prone.

Purpose of the Study:

• To develop a user-friendly tool for generating AlphaFold 3 (AF3) JSON input files, specifically for integrating glycan structures.
• To streamline the process of modeling glycans and their interactions with macromolecules using AF3.
• To reduce errors associated with manual JSON file creation for complex glycan architectures.

Main Methods:

• Development of JAAG (JSON input file Assembler for AlphaFold 3 with Glycan integration), a web-based graphical interface.
• Utilizing Chemical Component Dictionary (CCD) entries and bondedAtomPairs (BAP) syntax for glycan representation.
• Integration of glycan structures into the AF3 modeling workflow through simplified JSON file generation.

Main Results:

• JAAG successfully streamlines the creation of AF3-compatible JSON input files.
• The tool facilitates the accurate modeling of diverse glycan structures and their interactions.
• Reduced complexity and errors in preparing input files for glycan-macromolecule modeling.

Conclusions:

• JAAG significantly simplifies the integration of glycans into AlphaFold 3 (AF3) modeling.
• The developed interface enhances the accessibility and accuracy of glycan-macromolecule structure prediction.
• JAAG is a valuable resource for researchers studying complex biological systems involving carbohydrates.