Our goal is to model the key-mechanisms regulating subneuronal molecular signaling. Signaling is sustained by a complex network of molecular interactions involving thousands of different partners. Geometrical constraints, partners localisation, membrane composition, diffusion, crowding, short- and long-range protein-protein and protein-ligand interactions, internal protein dynamics and mutations combine all together and control the signaling. This is an intrinsically multiscale problem, both in space and time. To reach meaningful system sizes and simulation lengths, while achieving the relevant level of granularity, we develop statistical physics-based schemes bridging atomistic and mesoscale models as well as hybrid all-atom/coarse grained models.