Re: Protein folding and P = NP

From: Robert Myers (rmyers_at_rustuck.com)
Date: 01/23/04 

Date: Fri, 23 Jan 2004 03:21:55 -0500

On Fri, 23 Jan 2004 01:00:18 GMT, Mark Kvale
<kvale.nospam@pacbell.net> wrote:

<snip>
>
>For random polymers of amino acids, there is empirical evidence of a random
>energy landscape that does induce random glassy behavior in the
>conformational dynamics, but I don't know of any theorems proving that
>biologically realistic models are NP. You need to prove NP before finding a
>P folding algorithm and proving P=NP :)
>
Can anybody take a stab at explaining to me why anyone thinks this is
a comp.theory question, or that it can be reduced to P=NP?

There are dozens of approaches by which the protein folding are
attacked, they are all approximate, and I don't know that there is any
physically accurate formulation of the problem that fits into a set of
discrete solutions. There is some kind of energy landcsape, possibly
with discrete local minima, but the possible paths over local energy
barriers don't lend themselves to discrete optimization searches. If
you're thinking of something like a Hartree-Fock self-consistent
solution and looking for the ground (minimum energy) state, it may not
give you the right answer even leaving aside the inaccuracies in
Hartree-Fock.

You have to solve a time-dependent problem in quantum mechanics to do
protein-folding. What does that have to do with P=NP?

RM

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