The degree of similarity of two protein three-dimensional structures is usu
ally measured with the root-mean-square distance between equivalent atom pa
irs. Such a similarity measure depends on the dimension of the proteins, th
at is, on the number of equivalent atom pairs. The present communication pr
esents a simple procedure to make the root-mean-square distances between pa
irs of three-dimensional structures independent of their dimensions. This n
ormalization may be useful in evolutionary and fold classification studies
as well as in simple comparisons between different structural models.