protein folding

kresten no-sp at m.org
Thu May 17 01:58:08 EST 2001

Look up papers by Harold A Scheraga. Among his >1000 scientific publications
are some good ones on potential energy functions and new methods for finding
the global optimum in these. There is some interesting math in some of
these. If you are primarily interested in the optimization part you could
begin with the following review:

Wales and Scheraga
Global optimization of clusters, crystals and biomolecules
Science 288: 1368-1372, 1999

A recent paper on ab initio protein structure prediction using physical
properties only (PES optimization) can be found in:
Pillardy et al.
Recent improvements in prediction of protein structure by global
optimization of a potential energy function
PNAS 95(5): 2329-2333, 2001

I am sure that you can find references from these two papers to the more
mathematical oriented part and also for a detailed description of the
potential energy functions used.

Since this field is a highly important one there needs to be done things on
both the potential energy functions as well as the methods for finding the
global optimum in them. However, before you begin you should think about
what your goal is with solving "the protein folding problem" (what ever that
is...). Actually, I went to a lecture by Scheraga yesterday and his initial
remark was something along the lines of: "Today I am going to talk about the
calculation of protein structures. However, I must say that I do not think
that calculations are the best way to get structures. If you want a
structure, go measure it in the lab! The reason as to why we are dealing
with protein structure predictions is that they may help us understand the
underlying energetic principles in proteins. For this reason we only use
optimization of the potential energy function. We do NOT use methods such as
secondary structure prediction, threading or sequence alignment. We only use
physical properties."

Good luck

"Katerina Dimitrakopoulou" <katerina67 at hotmail.com> wrote in message
news:9dv5ci$44v$1 at usenet.otenet.gr...
> I study mathematics and I deal with optimization techniques. I know that
> the protein folding problem has to do with global optimization.  I am
> looking for the equations of the potential in protein folding problem in
> order to find the global minimum! i would be grateful if you could help
> please reply to
> katerina67 at hotmail.com
> thanks in advance

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