Covalentizer is a computational pipeline for creating irreversible inhibitors, starting from X-ray structures of known reversible binders.

The pipeline:
For a given reversible ligand bound near a free cysteine, we created a custom made, focused library of covalent analogs. We then used DOCKovalent to dock these tailored covalent libraries and calculated RMSD to find those which could bind covalently to the cysteine while keeping the main interactions of the original molecule.

We applied covalentizer to all of the liganded structures within the PDB, in which we found a ligand that binds near a free cysteine. All of these pre-calculated results are available in the form of a database of covalent candidates, and are updated weekly with new releases of the PDB.

You can also apply Covalentizer to your own structure (not found in the PDB).

If you find this useful, please Cite the manuscript describing Covalentizer.