I'm working on modeling covalently modified residues in Rosetta/PyRosetta. These modifications are things like acyl intermediates or covalent inhibitors...basically small-molecule ligands covalently bound to protein atoms in the context of a polypeptide chain. While the algorithm was written to model covalent inhibitors for a particular drug target we're working on, I'm interested in expanding it to look at a larger set of covalently-bound protein-ligand complexes in the PDB (both self-docking, cross-docking, and apo-docking).
This isn't exactly post-translational modifications, or non-canonical amino acids, or ligand docking, but sort of a combination of them. Does anyone know if the Meiler or Kuhlman labs (or anyone else in Rosetta) are working on ligand docking/modeling with covalent inhibitors where they explicitly model the covalent bond? If so, I'd like to get in touch.