clarification needed: scoring and procedure

[RaginSteveK]

1.] this phase's RMSD is the same mathematical procedure as the last phase ?? find the best possible alignment and count up the variations statistically- [ sum of squares, and all that....]??

2.] the sequence of amino acids is known- we're simply trying to stumble onto the best spatial arrangement..?? [but less stumbling than before]

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no improvemment was noted in the last part of phase 1 over the last 7 or 8 billions of structures generated: 11.19 or something was as good as it gets..

and we're below 5 already ??? !!!!

is this phase 2 protein any easier ??
or is this algorithm, and process, that much better ??

[ sorry to be critical; really not trying to be-- but couldnt we have gotten going on this billions of structures earlier.. as it became apparent that the analysis wasnt getting any more refined
..

any more refinements in the works ??? dont hold back !!

[[DPC]Mobster]

If I'm not mistaken that the last protein during Phase II was a completely different protein than the one we're researching now.
Those RMSD numbers are totally incomparable.

Ans yes the current algorithm and process is much better. That's why they called it Phase II :)

[tpdooley]

If this is the same protein that we were using during the Beta test; the best score that 50? of us were able to get was around 4.5A.
The same structure with 10 billion folds with the old client during phase 1 got around 7.11A

Wait until we've all folded for a week, and everyone's at least finished a whole 250 generations and see how low the score has dropped. :)

And we finished the beta testing (obviously we didn't identify all the bugs) in the middle of the 157structure protein. Howard probably wanted to finish the run so we'll have something to compare the run with..

[Brian the Fist]

This is the same protein as the beta test. Everything above is correct. :)