The equilibrium of complex systems often depends on a set of constraints. Thus, credible virtual reality modeling of these systems must respect these constraints, in particular for 3D interactions. In this paper, we propose a generic framework for designing assistance to 3D user interaction in constraints-based virtual environment that associates constraints, interaction tasks and assistance tools, such as virtual fixtures (VFs). This framework is applied to design assistance tools for molecular biology analysis. Evaluation shows that VF designed using our framework improve effectiveness of the manipulation task.