The post Human Genome Project era calls for reliable, integrated, flexible, and convenient data management techniques to facilitate research activities. Querying biological data that is large in volume and complex in structure such as 3D proteins requires expressive models to explicitly support and capture the semantics of the complex data. Protein 3D structure search and comparison not only enable us to predict unknown structures, but can also reveal distant evolutionary relationships that are otherwise undetectable, and perhaps suggest unsuspected functional properties. In this work, we model 3D protein structures by adding spatial semantics and constructs to represent the contributing forces such as hydrogen bonds and high-level structures such as protein secondary structures. This paper makes a contribution to modeling the specialty of life science data and develops methods to meet the novel challenges posed by such data.