I've been taking a quick peek at the graphics. I was wondering about how the lowest energy is calculated.

And why is it negative at times? How can you have a negative energy?

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Kathryn :o)
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Its just a comparaison with the native structure.

The native structure is the structure to be the structure with the less energy needed to be stable.

So its a comparaison and when you see a negative energy, its just because you have find a struture who need less energy than the native structure to be stable ..

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Maxxou59-Lille-France
Student at University of Chemistry

Its just a comparaison with the native structure.

The native structure is the structure to be the structure with the less energy needed to be stable.

So its a comparaison and when you see a negative energy, its just because you have find a struture who need less energy than the native structure to be stable ..

I don't think this is correct. I understand the structure with the energy minimum is the native structure. So there are no structures with less energy than the native one. That's why a search for the energy minimum works.

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I think that the native is the known structure who need the less energy, but the objectif of this project is to define some structure with part defined who needed the less energy and to for example represent a structure who can be used to make a new drugs ...

I think finaly that the point of view of a scientist is welcome is this thread ..

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Maxxou59-Lille-France
Student at University of Chemistry

If you all have time, I'd highly suggest watching this lecture by Dr. Baker. He discusses probably more than you want to know about how energy is calculated. . in addition to Rosetta as a whole:

http://norfolk.cs.washington.edu/htbin-post/unrestricted/colloq/details.cgi?id=449

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Before CASP7, we were given the native structure, and made comparisons between our predictions and the native structure. The RMSD (Root Mean Square Deviation) is a test of how close the atoms in our prediction were to the ones in the native structure. We don't have the native structure with CASP - so RMSD can't be calculated.

As for the energy calculation, we're working on the theory that the native structure will have a stable configuration with the lowest energy state. Our energy calculations, however, don't show a perfect arrow pointing down to low energy and low RMSD (when RMSD can be calculated). This means that there's room for improvement on the energy calculating algorithm. There's still a bit of art to picking out the structures to send in - eyeballing them and deciding which look possible. At least that's the impression I've received from the scientist's descriptions.

The reason the energy calculations on the lowest energy submissions is negative is that the energy algorithm is not setup for the native structure's energy to equal 0. While it may have been in the past, or may have had the zero energy spot arbitrarily set - it's been added to and changed since then that the best low energy structues are the most negative.

But that does bring up the question about what Rosetta's energy algorithm calculates for the some of the native structures we've had displayed on the front page?

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...why is it negative at times? How can you have a negative energy?

You guys seem to be missing an important point. I don't know how the Rosetta energies are calculated in detail, but in general, a negative total energy is exactly what makes the atoms stick to each other to form a protein. The atoms are hold together by attractive electrostatic forces. Whenever you have an attractive force field the potential energy is negative. The condition for an atom to be bound to a protein is that its total energy (the sum of its positive kinetic and negative potential energy) is negative. If you increase the kinetic energy of the atoms by heating the protein, the atoms will wiggle around faster and faster till they break their chemical bonds and the protein is destroyed and this will happen exactly at the point when the kinetic energy becomes large enough to cancel out all of the negative potential energy.

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And the light bulb goes on with the above post...


I was thinking in absolute values, not attraction and repulsion.


And I will watch that lecture.

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Kathryn :o)
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i had just *assumed* that the energy was calculated in log space, so that was why it was negative.