Among a wide range of applications, Circular Dichroism (CD) spectroscopy may be used to investigate the conformational changes of proteins. We describe the design of a visual framework for the analysis of data from automated CD spectroscopy. Based on a requirement description for model-based analysis of protein conformation changes, design choices for visual encodings and interaction techniques are explored and related to existing work in a different application. The results show how an entwined optimization and visualization can help to glean insights in molecular biophysics and protein chemistry.