A normalized root-mean-square distance for comparing protein three-dimensional structures

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.