Figure 2.

Different regions in the λ-REST2 simulations. The AZD4547-V555M complex is shown here as an example. The hybrid residue, denoted as the alchemical region, is depicted as a ball-and-stick model. It consists of disappearing (red) and appearing (blue) groups which are slightly separated for reasons of clarity. They can fully or partially overlap in the simulation as there are no interactions between them. The REST2 region, including the alchemical region (red and blue ball-and-stick), part of the ligand (orange bond), and surrounding protein residues (orange stick), is designated as the “hot” region. The selection of the REST2 region is described in the main text (section 2.3 REST2 region).