The ability to create “smart” molecular systems enables important applications in contexts where traditional electronic microcontrollers cannot be used. StableGen is an online tool for computing stable configurations of Thermodynamic Binding Networks. This computer-aided design tool can predict and simulate molecular system behavior at thermodynamic equilibrium, which can be used for research in medicine and synthetic biology. The ultimate goal for our tool is to enable researchers to design next-generation complex molecular systems ranging from logic gates to neural networks.