First, thanks for the reply Howard.

I am slowly wading through Principles of Biochemistry, by Horton et. al. and I downloaded your thesis a week ago and will finish chapter one soon. Incidentally, I was intrigued by your remark that if there are a finite number of folds that occur in proteins, and if they are all discovered in the nearish future, then ab initio folding schemes (schemes not relying on any prior knowledge of a protein or similar protein structure) would no longer be of interest, since the threading scheme should be able to reveal all remaining unknown protein structures. Might there still be a need for ab initio for designing brand new proteins?


Back to the thread... I understand RMSD to be the root mean square of the distances of each atom in the protein to where the atom is located in the protein's native fold. And yes, it is clear that RMSD is not available when dealing with proteins of unknown structure.

I was not clear in my suggestion about accelerating gen 0. I understand that the larger the set of structures in gen 0, the better the chance that the best structure of the lot will lead to the native fold in the 250 "improving" generations. Rather than reduce the 10,000 iterations in gen 0, I was hoping it would be possible to monitor the quality of each protein fold as it is being constructed, and if it becomes worse than the current best fold, then there would be no need to complete it. In other words, I meant interrupting individual folds, not the whole batch of 10,000.

I do, however, have two other suggestions/questions, one of which would try to reduce the number of iterations in gen 0. But I will read the threads in the educational forum before getting into those.


A couple of final, unrelated, questions (there was a sale on questions at the department store and I can't resist a bargain): I've never read any mention that there might be "useless proteins". I was just thinking, creatures evolve and are therefore in a state of flux. Is it fair to say that proteins go through gradual stages on their way to becoming very efficient? Or is it more likely that there are dramatic, random mutations, and presto, there's a nifty new protein in the species. And is it the case that some proteins that were needed by ancestors who are very different from the current creature are still produced, even though their function is no longer needed?


Yours in folding,
Michael Matisko