This paper explores structuralism as a way to model theories from scientific practice. As a case study I analyzed a theory about the dynamics of the basal ganglia, a part of the brain that is involved in Parkinson's disease. After introducing the case study I explore how to structurally represent qualitative assumptions about disease, intervention and dynamical systems in general. I further explicate the structure of the basal ganglia theory in detail, how it explains Parkinson's disease and how it implies treatments. I close with a consideration of how a structuralist representation could be useful in practice to explore and develop theories with the aid of a computer.