Homology models were prepared using the publicly accessible online Swissmodel programs, searching the SWISS-MODEL template library (SMTL version 2020-01-02, and PDB release 2019-12-27), or using a directed user-defined template approach. Coronavirus crystal structures are predominantly homodimers and were modelled as such, but the further refinement was initially performed on the monomeric forms. Newer releases of the Swissmodel software enable the inclusion of bound inhibitors when appropriate. In this case, models derived from PDB:2a5i included a bound covalent inhibitor. The initial heavy atomonly models were further refined using the Protein Preparation module in Schrödinger Suite 2019-2 to add hydrogen atoms and optimise the internal hydrogen bonding network. Finally, the models were energy minimised using the OPLS3e force field with charges from the force field and implicit water solvent, and the Polak-Ribier Conjugate Gradient (PRCG) method to gradient <0.05Å. The final minimised models were then analysed using MolProbity and visualised in Pymol v2.1. Molecular dynamics simulations were performed with the Desmond Molecular Dynamics System (D. E. Shaw Research, New York, NY) by using the tools incorporated in the Schrödinger Suite 2019-2. 24