Structural Systems Biology Toolkit (SSBtoolkit): From Molecular Structure to Subcellular Signaling Pathways
Journal of Chemical Information and Modeling, vol. 65, pp. 4257–4262
Abstract
Here, we introduce the Structural Systems Biology (SSB) toolkit, a Python library that integrates structural macromolecular data with systems biology simulations to model signal-transduction pathways of G-protein-coupled receptors (GPCRs). Our framework streamlines simulation and analysis of the mathematical models of GPCRs cellular pathways, facilitating the exploration of the signal-transduction kinetics induced by ligand-GPCR interactions: the dose–response of the ligand can be modeled, along with the corresponding change in the concentration of other signaling molecular species over time, like for instance [Ca 2+ ] or [cAMP]. SSB toolkit brings to light the possibility of easily investigating the subcellular effects of ligand binding on receptor activation, even in the presence of genetic mutations, thereby enhancing our understanding of the intricate relationship between ligand–target interactions at the molecular level and the higher-level cellular and (patho)physiological response mechanisms.
Authors 4
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Affiliation as printed
Department of Biotechnology
University of Verona
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Affiliation as printed
Computer Science and Natural Sciences RWTH Aachen University
Faculty of Mathematics
Forschungszentrum
IAS-5/INM-9
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Giulia Rossetti Aachen
Forschungszentrum Jülich · Universitätsklinikum Aachen · Jülich Supercomputing Centre · RWTH Aachen University
Affiliation as printed
Department of Neurology
Forschungszentrum
IAS-5/INM-9
Jülich Supercomputing Center, Forschungszentrum
University Hospital RWTH Aachen
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Alejandro Giorgetti corresponding
Affiliation as printed
Department of Biotechnology
Forschungszentrum
IAS-5/INM-9
University of Verona
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