How good is good (was Re: Comment to S.Blocklehurst (Re: Well, ...))

murphy kenneth p kpmurphy at blue.weeg.uiowa.edu
Fri May 5 09:24:16 EST 1995


In article <arneznehzdnajd5r at hodgkin.mbi.ucla.edu>,
Arne Elofsson <arne at hodgkin.mbi.ucla.edu> wrote:
>
....
>
>Every meeting I go to there is one or a couple posters that claims
>that they have solved the protein folding problem. Usually are these
>posters filled with some theoretical-computer-science-ai-crap. And then
>one table of data to show how close they can predict structures.
>
>Sometimes there is a small email adress at the bottom trying to sell you
>a program also. Well I guess we are not enough people out there that
>know that most of this is crap.
>
>arne
>
>PS. I know what thew question is, so if you know the answer 42, we should be happy.
>    My question is to given any sequence build a model to within 1.0 A from a crustal
>    structure. (At the moment I would be happu with 1.5 or even 2. (-: )
>
>-- 
>--------------------------------------------------------
>               From: Arne Elofsson
>         Email: arne at hodgkin.mbi.ucla.edu   			
>  WWW:  http://www.doe-mbi.ucla.edu/arne/main.html	

This brings up a question I've always had regarding structure prediction.  How
close do you have to be to the crystal structure to say you predicted it?  When
you say 1.0 A, do you mean for all atoms or just backbone?  What's the rmsd for
NMR and xtal structures of the same protein if you include all atoms and not
just backbone?

Regards,
Kip
--
Dr. Kenneth P. Murphy				e-mail: k-murphy at uiowa.edu
Department of Biochemistry			office: (319)335-8910
University of Iowa				lab:  (319)335-7936
Iowa City, IA 52242            		        FAX:  (319)335-9570



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