The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences.
The service is easy to use and upload your query to. There isn't a lot of customization for the analysis parameters but the results are clean and easy to understand.