Fig. 1.

Schematic representation of a GPCR (PDB IDs 5XEZ & 6LMK) in inactive (left) and active (right) conformations with an allosteric and peptide ligand bound, respectively. Large conformational changes occur upon binding of the peptide ligand and G_s-protein binding intracellularly, which represent possible dynamics that could be observed with Martin combined with Gō-models. The allosteric pocket in the transmembrane domain exemplifies the possibility to use Martini models for identifying transmembrane pockets, allosteric or cryptic, in various complex membrane compositions. Once a ligand is bound, backmapping is a possibility to obtain higher resolution information for further ligand optimisation or design. All figures were rendered using VMD (Humphrey et al., 1996).