*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
Hi Tommi, your points are well taken. I am well aware of such examples partly from my own work on helical cytokines which share the same fold with sometimes barely 10% seq.id. By structural similarity I meant structural agreement as judged by r.m.s.d values. Afterall, we often find that fold agreement does not necessarily mean that a structure can serve as a good model in MR approaches. My intention was actually to mention some of the original papers that formed the basis for the 'rule of thumb' that Marilyn Yoder wanted to know about. You are correct about the interpretation of fig 2 in the 1986 paper in EMBO J. and in fact this had already showed that this rule of thumb may be a bit too conservative. What we do need to point out, however, is that the plot in fig 2 arose from aligning core residues of the structures and not the entire structures. As one other contributor to the discussion pointed out, the alignment length is an important parameter when trying to draw conclusions about sequence divergence and structural similarity. And that is nicely illustrated in the more recent papers on the topic that have already been mentioned in the discussion. Best wishes Savvas -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tommi Kajander Sent: donderdag 22 september 2005 16:00 To: [email protected] Subject: RE: [ccp4bb]: sequence/structure homology *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** 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
