For the Covid Moonshot project, one question by Prof. Frank von Delft of Diamond XChem led to a series of events that culminated in
Fragmenstein, a module to do fragment mergers when the followup is as faithful to the starting crystal hits as possible. Even if it's intended use is the hit-to-lead process, there is a nice use that make it rather handy for computational biochemistry in general: switching the ligand in a PDB to another in an energy minimised fashion that obeys the original ligand.
