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Protein structure from scratch?

Tom Branham tbranham at mm.wellesley.edu
Fri Aug 5 10:27:57 EST 1994

Frank van de Loo (FJVAND00 at ukcc.uky.edu) wrote:
: Dear Modelers,
: This may be laughable, but I need to know.  Can one construct a model protein
: structure from scratch?  If one has a protein of a few hundred amino acids

Theoretically possible.  If you manage it, let us know, and we'll drive you
out to pick up your Nobel prize :-)

: length and various types of data (homology, site-directed mutagenesis,
: photolabelling, etc), and can come up with a hypothetical super-secondary or
: tertiary structure on paper for most or part of it, is it possible to constuct
: the model in a program that can then display it and be used for further
: refinement?  I have been trying to do this in Hyperchem, with much frustration
: since I can't fold the polypeptide about very well once I've made it.  Is there
: a way, or am I just trying to do something impossible?  All advice greatly
: appreciated!

Unless you are wil.ing to spend a few hundred years of your life, I would not 
spend too much more time trying to just fold it by hand.  Try to start looking
at structures for related proteins in the protein data bank to get some idea of
how the relatives are folded.  At least that will give you some kind of a 
starting point, or a reference frame.  past that you either have to break the
problem down into small changes from one of those structures, or start collecting
xray/nmr data  :-)  :-)  :-)

: Frank van de Loo
: USDA/ARS, University of Kentucky.

tbranham at mm.wellesley.edu

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