Is it just me, or does the energy get lower the more compact and spiral like the protein shapes are? I saw the top prediction looked rather spiraled without many straigt paths, and I also saw on my screen saver some of the lowest energies seemed to be similar. I saw one go lower then -500 and it was a pretty spiraled shape, and relatively compact.

Is it just me, or does the energy get lower the more compact and spiral like the protein shapes are? I saw the top prediction looked rather spiraled without many straigt paths, and I also saw on my screen saver some of the lowest energies seemed to be similar. I saw one go lower then -500 and it was a pretty spiraled shape, and relatively compact.

That largely depends on the nature of the residuals attached to the backbone. These residuals have different chemical properties and can either attach to one another, repell each other or also attach to water. Then it's is a question of how flexible the backbone is.

Proteins often have (at least stretchwise) spiral shapes that are entwined to each other and look like tangled balls of wool. Beneath that structure, you will find other (shorter or longer) motifs, the most prominent of which are called "alpha-helices" and "beta-sheets". How these motifs follow each other has a big influence on what overall structure the protein can adopt.

Quote from the science FAQ:

What forces determine the unique native (most stable) structure of a protein?

The sequence of amino acids is sufficient to determine the native state of a protein. By virtue of their different chemical properties, some amino acids are attracted to each other (for example, oppositely charged amino acids) and so will associate; other amino acids will try to avoid water (because they are greasy) and so will drive the protein into a compact shape that excludes water from contacting most of the amino acids that "hide" in the core of this compacted protein.

So, finally it is easy to make a prediction of how a short sequence of a protein is likely to form 3-dimensionally, but hard to predict what happens when it gets in contact with water, other parts of the same protein or even other proteins.

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"I know that you believe you understand what you think I said, but I'm not sure you realize that what you heard is not what I meant." R.M. Nixon

Ahh thank you for that very informative reply, and your nice photo of Saturn Christoph! I wish my Saturn images turned out that well! :) Happy DC'ing to you!

Ahh thank you for that very informative reply, and your nice photo of Saturn Christoph! I wish my Saturn images turned out that well! :) Happy DC'ing to you!

Thank you, I use an ETX125, tiny but fine optics. And: welcome to Rosetta, although you seem to be onboard some hours longer than I am.

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"I know that you believe you understand what you think I said, but I'm not sure you realize that what you heard is not what I meant." R.M. Nixon