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World Community Grid Forums
Category: Completed Research
Forum: Human Proteome Folding - Phase 2
Thread: folded structures per protein |
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Thread Status: Active Total posts in this thread: 2
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
I am not sure if this has been answered before or not. On David Baker's Rosetta site, he explains that the more structures we explore for a particular protein, the more likely one of those structures is to find the lowest energy state and be the closest to the actual protein structure. (http://boinc.bakerlab.org/rosetta/rah_welcome.php )
I remember reading somewhere else (perhaps on his site also) that optimally, this is in the 100,000+ structure range for any given protein (with the structures varying by different random seeds?). I was wondering how that tied into HPF2 (and quorum)? Do we use (let's say) 50,000 different "random" seeds for the structure, with a quorum of three on each seed?  |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hi arcane63,
Dr. Baker points out that if each amino acid is allowed 3 states of rotational freedom (and in reality there are more) then a protein with 100 amino acids presents us with 3 to the 100th power possibilities to explore. Keeping that in mind, I think that each work unit comes with its assigned random seed and with a required number of . . what shall I call them? - iterations. Right now we have withdrawn HPF2 while we put in all the bug fixes that the Baker Lab has made in Rosetta these last few months. I am uncertain whether or not this changes the basic algorithm any, but I strongly suspect that there are some fairly major changes. Lawrence |
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