Similarities between protein 3-D structures.

A simple, new, systematic method has been developed to evaluate the structural similarity of proteins. Firstly, similar protein fragments of a definable length are detected, combined in pairs and superimposed. The fits are improved until a maximum number of C alpha atoms show a distance below a given threshold value. The final number of matching C alpha atoms can be used to quantify the similarity of protein folds and to identify the best superposition of two proteins. using this procedure a systematic search for structural similarities of proteins in the Brookhaven Protein Data Bank was performed. The results of these investigations allow us to divide the proteins into 182 structural families and to estimate the relationships between single members of the classes found.