CHARMM-GUI adds a web module that automates covalent ligand docking
- CGUI-CLD is a new CHARMM-GUI module that automates ligand preparation, ligand modification and docking runs for covalent ligands, built on AutoDock4.
- A knowledge-based library covers 66 warheads and 8 amino acids, so the post-reaction ligand geometry no longer has to be built by hand.
- Results are presented through a browser interface.
💡 Points
Covalent docking is where my own campaigns stall: building the bonded adduct for each warhead is tedious, so I triage by intuition. A browser tool that handles it would let me rank a whole warhead set against a cysteine pocket in an afternoon. Docking scores won't capture reactivity, so I'd still pair this with kinetic data.
CHARMM-GUI Covalent Ligand Docker as a Web-Based Molecular Docking Platform for Covalent Ligands ↗