Protein folding

Hans Beernink hbeernin at med.uvm.edu
Thu May 2 14:45:52 EST 1996


David Micklem (drm21 at mole.bio.cam.ac.uk) wrote:

: What I have is the NMR structure of a particular protein domain.  I also
: have the sequence of several (many) similar domains which show a high
: degree of sequence homology to the one whose structure has been
: determined.  What I want to do is to see how well these homologues 'fit'
: the determined structure.  If this could be used as the basis for a search
: for a 'local' most-likely stable structure, then so much the better.  Of
: course, if the sequence provided _couldn't_ stably form the template
: structure, or anything close, that would be interesting too.  And if it
: could interpret the results and  write up a couple of papers for me
: too.... 


David- it sounds like you need to do some molecular dynamics.  There are 
some (relatively) user friendly packages (e.g. insight with the discover 
module, xplor etc.) that will allow you to "thread" your AA sequence into 
a structure coordinate file.  After minimizing your structure, you can 
compare the results with the original "anchor" structure and make some 
predictions.  

Best regards, 
Hans

--
_____________________________________________________________________________

"The worst monotonous drone coming from a lectern or the most eye-splitting
textbook written in turgid English is nothing in comparison to the 
psychological Sahara that starts right in your bedroom and spurns the 
horizon."

	-Joseph Brodsky, from "In praise of Boredom"
	 delivered as a commencement address at Dartmouth College.
_____________________________________________________________________________
Hans T.H. Beernink, Department of Biochemistry, University of Vermont

hbeernin at protein.med.uvm.edu			FAX (802)862-8229 
hbeernin at zoo.uvm.edu				Tel.(802)656-8244
		URL http://moose.uvm.edu/~hbeernin/
		URL http://salus.med.uvm.edu/biochem/



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