SSB toolkit: from molecular structure to subcellular signaling pathways.

Abstract

We present, here, an open-source systems biology toolkit to simulate mathematical models of the signal-transduction pathways of G-protein coupled receptors (GPCRs). By merging structural macromolecular data with systems biology simulations, we developed a framework to simulate the signal-transduction kinetics induced by ligand-GPCR interactions, as well as the consequent change of concentration of signaling molecular species, as a function of time and ligand concentration. Therefore, this tool brings to the light the possibility to investigate the subcellular effects of ligand binding upon receptor activation, deepening the understanding of the relationship between the molecular level of ligand-target interactions and higher-level cellular and physiologic or pathological response mechanisms.