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Quantitative comparison of two structures of the same biological macromolecule or complex is a very common but by no means trivial task. One such example is the comparison of a model with the experimentally determined (reference) structure.
(Olechnovic and Venclovas 2014) The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes. Nucleic Acids Res.