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Originally posted by Michael H.W. Weber
3. Any (preliminary) news on the CASP results? I wonder why such drastic changes of the algorithm are undertaken (not satisfied with the current results?).
Michael.
i will look for the quote from howard (or he can jump back in here and repeat it himself), but howard posted that changes are needed to refine the process to be more competitive (ie get better results) with the other processes that turned in results to the CASP thingy (ok , i admit it, the science is all way over my head :crazy: )
any way, i will go look for the quote, hold on
here we go, i think you can get the idea from these 3 quotes
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We will post a complete 'report' as soon as we have gone through all the relevant numbers. While I can tell you we did not 'win', we appear to have done reasonably well considering our algorithm is still in its infancy compared to many of the other participants. Clearly brute force alone is not sufficient to predict protein structures but in combination with a 'smart' algorithm we believe it can far exceed what anyone else will be able to do without DC. As we continue to test new enhancements to our current basic algorithm and scoring functions, we expect to see great improvements in our ability to sample structures and pick out low energy ones.
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As for the new method, I am busy coding it now as we speak, the new infrastructure I'm putting in will allow us to try several different ideas, all sharing the common idea of iteration. i.e. make some structures locally, then take the best one(s) and do something with it to then make more structures, etc. Thus there will be a lots less uploading to the server but occasional downloading as well. Most changes will be invisible to the user though. We'll keep you posted as it develops.
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Our current plan is to improve the sampling from 'random' structures to doing it more intelligently. We shouldn't need to sample 10 billion structures to get what we are getting, if we do it a bit more intelligently. Massive computational resources will still be required though
it seems to me (in my simple way) he is saying that improvements need to be made to get better results
for those involved from the beginning (about 1 year ago), howard has always intimated that this was a work in progress and that the science may dictate changes, after all what is the goal? to figure out a better way to do this folding stuff, right? :)