We introduce a new measure for comparing protein structures that is especially applicable to analysis of molecular dynamics simulation results. The new measure generalizes the widely used root-mean-squared-deviation (RMSD) measure from three dimensional to n-dimensional Euclidean space, where n equals the number of atoms in the protein molecule. The new measure shows that despite significant fluctuations in the three dimensional geometry of the estrogen receptor protein, the protein's intrinsic contact geometry is remarkably stable over nanosecond time scales. The new measure also identifies significant structural changes missed by RMSD for a residue that plays a key biological role in the estrogen receptor protein.
Shibberu, Yosi; Holder, Allen; and Cooper, David, "Intrinsic Contact Geometry of Protein Dynamics" (2010). Mathematical Sciences Technical Reports (MSTR). 24.