Posted on 12/08/2008 12:10:04 PM PST by texas booster
... We present a novel computational approach for describing the formation of oligomeric assemblies at experimental concentrations and timescales. We propose an extension to the Markovian state model approach, where one includes low concentration oligomeric states analytically. This allows simulation on long timescales (seconds timescale) and at arbitrarily low concentrations (e.g., the micromolar concentrations found in experiments), while still using an all-atom model for protein and solvent.
As a proof of concept, we apply this methodology to the oligomerization of an Abeta peptide fragment (Abeta 21–43). Abeta oligomers are now widely recognized as the primary neurotoxic structures leading to Alzheimer's disease. Our computational methods predict that Abeta trimers form at micromolar concentrations in 10 ms, while tetramers form 1000 times more slowly. Moreover, the simulation results predict specific intermonomer contacts present in the oligomer ensemble as well as putative structures for small molecular weight oligomers. Based on our simulations and statistical models, we propose a novel mutation to stabilize the trimeric form of Abeta in an experimentally verifiable manner.
I have nothing but respect for long-time folders that got their points the hard way. From what I’ve read, the reason GPUs are capable of such a high Points-Per-Day is not only that modern GPUs are quite powerful, but also because the GPU work units are different. The GPU work is considered more valuable by Stanford, so they bumped up the points to encourage people to do GPU folding. The same is true of the Playstation 3 work, but I believe they actually lowered the points for that work (they arbitrarily chose 1000 PPD) because otherwise the casual PS3 folders would crush everyone else. Even now I think most of the FLOPS come from PS3 users.
By the way, if anyone has a Facebook account, there’s an application that lets you track your points on your profile. I just joined and I’m the only team member right now:
http://apps.facebook.com/proteam/showteam.php?team_id=36120
Not to take away from general purpose CPUs. There are certain calculations that cannot be done by GPUs that tie the entire project together. Both are needed to advance science.
I also suspect that if Stanford could convince Sony to change the PS3 to that it ran F@H in the background 24/7 that Stanford would leap for joy. Imagine the FLOPs if 3,000,000 PS3's joined the project. Wow.
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Just joined the Facebook page.
I’d like to hear more about your system. In 6-7 days you have more points than my 3 years of folding.
self ping for home
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