Pseudo-energy comparison question?

[Digital Parasite]

Howard/Elena:

Already with this new protein we are now down to a 6.16 pseudo-energy value. Does a pseudo-energy value depend on the size of the protein you are looking at so a 6 value on this small 100AA protein doesn't necessarily mean it is much better than a 40 value on the previous larger protein or are we kicking butt on this current one?

Thanks,
Jeff.

[Brian the Fist]

The pseudo-energy term is only a very rough indication of how good the structure MIGHT be. If it were accurate and reliable, we'd have already solved the protein folding problem (which we haven't). All it tells us for sure is that the structure is compact, has secondary structure (helices and sheets) comparable to that predicted, and it has many energetically favourable contacts. To answer your question though, it should only have a very weak dependence on length. We need to manually inspect some of the better pseudo-energy structures and subject them to some furtehr analysis still.