AlphaFold3 Covalent Ligand Generator

This tool helps generate JSON input files for AlphaFold3 with covalent ligand-protein interactions. The tool now includes pattern-based suggestions for common reactive groups to help identify the correct atom for covalent bonding.

Name for this prediction:

Protein Sequence:

DNA Sequence(s) (one per line):

Ligand SMILES:

Common Reactive Group:

Ligand Atom ID for covalent bond: This is the atom ID in CCD format that will form the covalent bond

Ligand Name (3-letter code):

Protein Residue Number (for covalent bond):

Protein Atom (for covalent bond, typically "SG" for Cys):

Model Seeds (comma-separated integers):

Output JSON:

JSON will appear here after generation.

AlphaFold3 Covalent Ligand Generator

Suggested Reactive Atom

Output JSON: