an interesting way to compare structures from the same protein sequence is reported here :

acta cryst D56 714-721, 2000 "objective comparison of protein structures : error-scaled difference distance matrice"

acta cryst D60 2269-2275, 2004 "domain identification by iterative analysis of error-scaled difference distance matrices"

both are by T. Schneider, might find a couple others out there

HTH

-bryan

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