Originally posted by Blackout
Hello,

I have a few questions about how energy and best structure are determined.
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Just a 'few' questions huh? Sounds like you need a Biochemistry text book, or perhaps a read of Chapter 1 of my thesis is in order (available on the About->Stuff section of the web site). I'm not going to give you a biology lesson here but I'll try to briefly address some of your questions. See the educational section in this forum as well (make sure you set it to view ALL messages).

The best structure in gen. 0 is the best 'score' - a combo of compactness, secondary structure accuracy to prediction, and pseudo-energy. Energy is a contact energy similar to many commonly used in the protein folding field and is quick to compute, from residue pairs close together in space interacting.

The pseudo-energy cannot be computed until the protein is completely built. See the Results section of the website for sample energy vs RMSD plots. RMSD 0 = folded, RMSD 20+ = unfolded.

I am not sure if you understand what RMSD is or not, so you might need clarification on this as well. We are currently folding proteins whose true structure is already known but for true prediction, you cannot compute RMSD (the distance to true structure).

I also think you miss understand the point of how this present algorithm works. Gen. 0 acts to seed the simulation - find a suitable starting point for the rest of the simulation. To make it shorter would be foolish as it would lessen our chances of finding a good starting structure and thus ruin the whole 250 generations if chosen poorly. On the other hand, we can almost guarantee a 'decent' starting structure will be found in 10000 samples. We do not know beforehand what a 'decent' score will be though, so we must just make our 10000 and take the best. Energy scores can vary widely from protein to protein in magnitude.

Hope this clears things up a bit and points you in the right direction for further reading.