Root mean square deviation
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The root mean square deviation (RMSD) is the measure of the average distance between the backbones of superimposed proteins.
Where δ is the distance between N pairs of equivalent atoms (usually Cα and sometimes C,N,O,Cβ).
Typically RMSD is used to make a quantitative comparison between the structure of a paritally folded protein and the structure of the native state. For example the CASP protein structure prediction competition uses RMSD as one of its assessments of how well a submitted structure matches the native state.
Also some scientists who study protein folding simulations use RMSD as a reaction coordinate to quantify where the protein is between the folded state and the unfolded state.
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