[RC5] Gene sequencing next d.net project?

Martin Hecko martineno at hotmail.com
Sun Dec 5 11:33:34 EST 1999

>I love the idea but what exactly do you propose?
>I myself have been toying with the idea of 3D Protein Structure
>analysis.  The problem is huge and I'm just trying to decide how you
>would split the analysis into distributable packets which could be
>divided and integrated.  I think d.net could do wonders for that sort of
>analysis.  If anyone has any ideas on how to go about with the division
>of the problem, I'd love to hear it.

If you look into the archives of this mailing list you will find that the 
protein folding has been suggested. The thread is here:


I quote one particualarly informative mail:

----begin quote
Ronald Van Iwaarden (rrt0136 at ibm.net)
Thu, 26 Feb 98 17:17:18

On Thu, 26 Feb 98 15:17:48 -0600, gindrup at okway.okstate.edu wrote:

>The rules are sufficiently well known. How do you distribute it? Each 
>client has to have a whole protein and at that point it takes a *long* time 
>for that client to fold the protein. If we break it into functional units 
>distributed across clients, the problem is again communications bandwidth.

The protein folding problem can be stated as a global minimization
That is, find the lowest energy configuration given that it can take on a  
continum of different configurations. This problem can then be solved using 
a branch and bound technique based on interval arithmetic. I have software 
that does the branch and bound and am presently working on writing a  
general parallel framework for it at this time.

In many ways, it is very similar to how we have solved DES or RC5, you
request a region of the space and search it. If someone else informs you of 
a better energy configuration than exists in your region (this can be 
rigorously verified on finite precision machines like our computers), you 
prune your region and then request another region to search. This can either 
be set up as a client server system like d.net uses but could tend to be 
inefficient and it is better to organize it as a group of machines, each 
requesting boxes from eachother. Early on in the search, communication is 
relatively low but as you get closer to finding the true solution, 
communication increases rapidly, similarly to how communication almost 
certainly increased while doing DES-II when we grew close to the end.

-----end quote

(the sunny side of life)


The question seldom addressed is *where* Medusa had snakes. Underarm hair is 
an even more embarassing problem when it keeps biting the top of the 
deodorant bottle.
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