Biology Comp. Sci. / Eng. Evolution Intelligent Design

Quantum Leap In Protein Folding Calculation

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http://www.sciencedaily.com/releases/2006/09/060918202123.htm

Applying techniques derived from classical and quantum physics calculations may radically reduce the time it takes to simulate the way that proteins fold.

It’s vital to understand the shapes that proteins take on as they fold up because the shapes determine how they function, both in keeping cells running and in leading to various diseases.

Rather than calculating the motions of a protein molecule step by step, as most simulations do, a team of Italian and French physicists studied the evolution of a molecule using variational principles. The technique allowed the physicists to evaluate all the possible paths that the molecule’s parts would follow and then pick out the most likely one.

As a result, they expect to streamline protein folding calculations from trillions of steps to hundreds. The improvement is significant because conventional protein folding simulations that currently require supercomputers or large PC farms could instead be solved with individual desktop PCs running variational principle calculations.

The researchers explain that the new application of the old physics method is faster because it allows them to spend less time calculating motions of molecules stuck in quasi-stable intermediate steps along the folding process. The intermediate steps account for vast amounts of wasted computation time in traditional, step-by-step simulations.

I thought this bit of news pertinent to UD considering that one huge limitation with computer simulations is that they do not reflect biological reality. Perhaps this will help.

6 Replies to “Quantum Leap In Protein Folding Calculation

  1. 1
    jpark320 says:

    I can’t wait to hear their excuses once they figure out its impossible again…

  2. 2
    Chris Hyland says:

    “The improvement is significant because conventional protein folding simulations that currently require supercomputers or large PC farms could instead be solved with individual desktop PCs running variational principle calculations.”

    I’ll believe it when I see it.

  3. 3
    Douglas says:

    I have a question: Selection in Evolution first becomes “applicable” at the protein level, right? I mean, it’s first at the protein level that “fitness” becomes an issue, isn’t it? That is, a mutated gene doesn’t affect anything, except insofar as it affects the protein it codes for, n’est pas? (Correct me if I’m wrong, but pretend I’m insightful anyway.)

    One thing I’ve been pondering is how various proteins could have arisen from other or “earlier” proteins. If the particular shape of a protein is fundamental to its function, then is it possible to show that some classes, or instances, of proteins are several “steps” (topologically) removed from other classes or instances of proteins? Am I making any sense?

  4. 4
    Jehu says:

    Douglas, I think you are making the argument thatn Dr. Sean Pitman discusses here http://www.detectingdesign.com/steppingstones.html

  5. 5
    Douglas says:

    Jehu,

    Thanks for the link. I printed out, and read, the article, and I think his idea is very significant. The increasing improbabilities of randomly generating “beneficial” proteins or features seems to be another impossibility Evolution must magically overcome. But it wasn’t exactly the point I was getting at regarding the topology of proteins (although I’m not sure my point has any actual merit).

  6. 6
    Zero says:

    The way my calculations work out,
    infinity (folded once) = zero.

    Jhn 10:16 And other sheep I have, which are not of this fold: them also I must bring, and they shall hear my voice; and there shall be one fold, [and] one shepherd.

    Zero

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