A normalized root‐mean‐spuare distance for comparing protein three‐dimensional structures

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Abstract
The degree of similarity of two protein three‐dimensional structures is usually measured with the root‐mean‐square distance between equivalent atom pairs. Such a similarity measure depends on the dimension of the proteins, that is, on the number of equivalent atom pairs. The present communication presents a simple procedure to make the root‐mean‐square distances between pairs of three‐dimensional structures independent of their dimensions. This normalization may be useful in evolutionary and fold classification studies as well as in simple comparisons between different structural models.