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Many programs have been designed to view the 3D structures of protein molecules in 2D. However, three types of linked information haven't been previously defined in a systematic way that highlights the interface design challenge. Specifically, a scientist must have sequence, structure, and homology information in working memory to manipulate and understand a protein structure or related protein structures. Categorizing information types enables the application of classical interaction principles to the design of an intuitive interface for both expert and novice users. In a comparative user evaluation, their Molli system enhances the exploratory process of manipulating proteins of varying complexity by preserving the underlying data's linkages and relations.