AlphaFold3 Covalent Ligand Generator

This tool helps generate JSON input files for AlphaFold3 with covalent ligand-protein interactions. Note: This is a simplified client-side version that creates a template JSON file. For complete functionality including 3D coordinates and proper CCD formatting, you would need to process this with RDKit offline.

Name for this prediction:

Protein Sequence:

DNA Sequence(s) (one per line):

Ligand SMILES:

Ligand Name (3-letter code):

Protein Residue Number (for covalent bond):

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

Ligand Atom ID (for covalent bond): Note: This should match the atom ID in the generated CCD format. When processing offline with RDKit, verify the atom IDs.

Model Seeds (comma-separated integers):

Output JSON:

JSON will appear here after generation.