So being A average blue collar worker. I need to understand the low energy states. I understand the lower the number even into negative intergers is what we realy want. Guese my question is just how low into the negative numbers is where we find the true state of the protien. I know i have seen numbers in the negative 60s or lower on alot of the Casp7 WUs i have been running.

Humm on a follow up will the true state alwasy be a negative number or could it alos be a positive one

---

So being A average blue collar worker. I need to understand the low energy states. I understand the lower the number even into negative intergers is what we realy want. Guese my question is just how low into the negative numbers is where we find the true state of the protien. I know i have seen numbers in the negative 60s or lower on alot of the Casp7 WUs i have been running.

Humm on a follow up will the true state alwasy be a negative number or could it alos be a positive one

Hi Charlie,

a good question, as the numbers are not provided with any units like calories or joules. I've asked myself what the units would be too. But even without knowing units I'll try an answer.

Think of it that way (like the planet analogy used here): Every single shape the protein can adopt has its own energy. How much that is depends on how much energy you have to apply to bend the model you started from and how much energy is set free by the bonds it then forms. If you would make a horizontal map of every shape the protein can take and would plot the energy corresponding to each shape vertically, you would get a bumpy surface like a sandbox that children played in a lot.

Some bumps go up because bending the shape that way takes more energy than the new bonds set free (like trying to put two magnets together that are on opposite ends of a spring: if the spring is too strong the magnets are torn apart again), some will go down because you get more energy from the bonds formed than the bending takes.

Every bump that goes up (that has positive energy) means you have a higher energy than the model you started with. This means it is going to be less stable than the starting model. To take the sandbox analogy: if you put a ball on the bump that is going up, it is going to roll down again. So the structure you are searching for will definitely have an energy that is lower than the starting model and is associated with a negative number in your screen savers "accepted energy" display.

How low that energy is going to be is hard to predict. It depends on the size of the protein and of the ways it can form bonds. But from what I've seen and from my intuition as a chemist I would say that the scale is such that the numbers you see lie in the low hundreds (maybe also a little below 100) for small proteins and may go up to 1000 and higher for bigger proteins.

Have you ever seen one of those funnel shaped machines you put a quarter into at the top and it spirals around and around until it finally falls through the hole at the bottom?

That's essentially what this program is doing. Each work unit drops a quarter somewhere on a 'planet' covered by these spiral-quarter-machine-funnels. Some funnels are deeper than others, but once it’s in one, it can't climb back out. Rosetta keeps spiraling around, getting lower and lower, until it falls into the hole at the bottom. . this is the low energy for that work unit.

The energy is just a way of measuring how deep a hole is, like sticking a yard stick down the middle. Deeper holes have a more negative number (like saying your swimming pool is -6 feet tall).

Bigger (longer) proteins beget bigger 'planets' and deeper spirals. . . therefore lower energies.

That’s how I look at it anyway :)

-Ethan

---