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Function is a dynamic property closely related to the conformational mechanisms of the protein structure in its physiological environment. Efficient methods and tools for predicting collective motions at the molecular level are becoming increasingly important for understanding and controlling the function of target proteins. The molecular motions of proteins in different mode types are determined in the present study using the Gaussian network model (GNM). Based on GNM, we present a system that enables efficient query and visualization of protein dynamic behaviors such as mode shapes and 3D mobility structures.