The complexes 4W5O (Ago2), 7M5O (Cas12j) and 6GPG (RIG-I) were downloaded from the PDB (Protein Data Bank) . The missing nucleotides in the PDB model 4W5O were built manually in PyMOL (Version 2.5.1) (The PyMOL Molecular Graphics System, Version 2.4 Schrödinger, LLC). The missing loops in the protein structure were modelled in BioLuminate , and afterwards the built loops were refined using Prime ) . Both terminal phosphates were deleted from the ends of RNA molecules. The bounds ions (Zn and/or Mg) were retained. The models were prepared in Protein Preparation Wizard : the water molecules were deleted beyond 5.0 Å from het groups, the states of het groups were generated using Epik in pH 7.4 ± 2.0; the optimization of H-bonds was performed with PROPKA in pH 7.4 followed by restrained minimization of them in OPLS4 . The N-terminal of the proteins were not present in the crystal structures and they were omitted which is why Ago2 residue numbering starts from 22, Cas12j starts from 53 and RIG-I starts from 29. All systems were then converted to Amber atom names using the pdb4amber script in the AmberTools21.