Due to the limitations of existing experimental methods for capturing stereochemical molecular data, there usually is an inherent level of uncertainty present in models describing the conformation of macromolecules. This uncertainty can originate from various sources and can have a significant effect on algorithms and decisions based upon such models. Incorporating uncertainty in state-of-the-art visualization approaches for molecular data is an important issue to ensure that scientists analyzing the data are aware of the inherent uncertainty present in the representation of the molecular data. In this work, we introduce a framework that allows biochemists to explore molecular data in a familiar environment while including uncertainty information within the visualizations. Our framework is based on an anisotropic description of proteins that can be propagated along with required computations, providing multiple views that extend prominent visualization approaches to visually encode uncertainty of atom positions, allowing interactive exploration. We show the effectiveness of our approach by applying it to multiple real-world datasets and gathering user feedback.