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Regarding the issue that 3D protein structure similarity determination requires a lot of computing time, this paper proposes a 3D protein structure consistency comparison using 2nd PCA (second principal component analysis). Mainly through 3D protein structure distance matrix to compute the corresponding PCA2 value, define their similarity by the PCA2 ratio of the two protein structures to be compared. This method does not require pre-registration for the protein backbone. Through a series of tests to verify that, by guaranteeing certain accuracy, this method greatly improves the speed of the similarity comparison.