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On Thu, 22 Sep 2005, Savvas N. Savvides wrote: > In that paper you will also find a plot of r.m.s.d vs sequence identity > which reveals that the 3 angs rmsd (which we generally take as an > upper-boundary for structural similarity) occurs at about 25-30% seq.id. > > Best wishes > Savvas > -I dont think this true a) personally i know explames -at least beta-propellers with seq id less than 15% and rmsd around 2 A, and i am sure many more. b) If you check the EMBO J Chothia paper (cant find it now, but the same data is in Creightons book) you see rmsd 2 A occurs below 20% identity. The other question is what do you mean by structural similarity? surely proteins can have the same fold wihtout practically any >20% seq. identity ---if this about feasibility of use as a molecular replacement, but thats another thing. Tommi
