Why F@H; Alzheimer's Simulation work published

[LCB001]

This is why I F@H.

From the blog of Prof. Vijay Pande: Folding@home

December 08, 2008

Folding@home Alzheimer's Simulation work published

I am very happy to announce that a first key work (paper #58 at http://folding.stanford.edu/English/Papers) from the Folding@home project on Alzheimer's Disease (AD) was just published

Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach, by Nicholas W. Kelley, V. Vishal, Grant A. Krafft, and Vijay S. Pande. J. Chem. Phys. 129, 214707 (2008); DOI:10.1063/1.3010881

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Abeta misfolding and aggregation is believed to be the cause of Alzheimer's Disease. Simulations, like Folding@home, are a natural way to understand this process. However, there are several key challenges for simulating the key step -- oligomerization. This work represents a new way to simulate Abeta oligomerization, with a key advance of being able to simulate experimentally relevant timescales and concentrations, using a novel method. We use this new method and the power provided by Folding@home donors to simulate oligomerization in all-atom detail. This has lead to specific predictions about the process, which we are now testing experimentally.

In many ways, this paper is the "tip of the iceberg" for the Folding@home activities in AD, with a lot more interesting results to come, especially in terms of experimental tests of our predictions and interesting new possibilities for new drugs and AD therapeutics. So, while we're excited that this result is now past peer review, we're even more excited for what's coming down the pipeline, waiting peer review. We'll keep you posted as more results become public, hopefully with some even bigger announcements in 2009.

UPDATE:
It was asked which clients participated. This work started several years ago and took some time to analyze and then publish. So, it ran exclusively on classic clients. For the follow up simulations, we are using a mixture of GPU, SMP, and classic clients. Due to the large number of classic clients, they allow us to calculations not possible on the other platforms. However, the raw speed (but smaller number) of the GPU and SMP clients allow us to get a good rough idea quickly, refining later with classic clients.



Posted at 10:33 AM in Science | Permalink | Comments (3)

I can't wait to see what results the SMP and GPU clients will be able to generate...

Edit// Added Update

December 18, 2008

New FAH results on possible new Alzheimer's drug presented

This is very preliminary news, but something I'm very, very excited about, so I'll give some advance news. On Tuesday, we presented our results regarding new possible drugs (small molecule leads) to fight Alzheimer's Disease at a recent meeting at Stanford. This meeting was part of the NIH Roadmap Nanomedicine center (Center for Protein Folding Machinery) retreat and was supported by NIH grants to Folding@home.
It's very early (so we are not publicly talking about the details until this has passed peer review), but we are very excited that it looks like we may have multiple small molecules which appear to inhibit toxicity of Abeta, the protein which is the toxic element in Alzheimer's Disease.

This is exciting in many ways. It's been a long road for FAH to get to this point, but we are starting to see the possibility of seeing these results published easily before our 10th birthday (October 2010). Considering all the technology development that had to be done in the first five years, these results have come very quickly (in the last 3 years), which is exciting. In particular, we are now looking to apply these methods to other protein misfolding diseases (we have pilot projects for Huntington's Disease underway).

Finally, I should stress that while we're very excited about this, it's still early and a lot can go wrong between where we are and having a drug that doctors can prescribe. Over the holidays, we will be double checking the experimental data, crossing t's and dotting i's to make sure there is nothing missed before we think about submitting this for peer reviewed publication. Also, there is still a long way from an interesting possible drug (where we are now) to something which has passed FDA clinical trials (where we'd love to be), and a lot can go wrong in clinical trials in particular.

Thus, this is an important milestone for FAH and we are very grateful to all who have contributed. Happy holidays to all!

[3.0charlie]

We so totally rock.

[BrainEater]

Wewt !

[chrisk]

Looks like our clients are starting to get some real work done :)

[Exmortis]

Fold for the future!

[Dashock]

Good Job guys!


We Need more for the Fight!

[LCB001]

Update from the blog of Prof. Pandes, I have added this to the first post

December 18, 2008

New FAH results on possible new Alzheimer's drug presented

This is very preliminary news, but something I'm very, very excited about, so I'll give some advance news. On Tuesday, we presented our results regarding new possible drugs (small molecule leads) to fight Alzheimer's Disease at a recent meeting at Stanford. This meeting was part of the NIH Roadmap Nanomedicine center (Center for Protein Folding Machinery) retreat and was supported by NIH grants to Folding@home.
It's very early (so we are not publicly talking about the details until this has passed peer review), but we are very excited that it looks like we may have multiple small molecules which appear to inhibit toxicity of Abeta, the protein which is the toxic element in Alzheimer's Disease.

This is exciting in many ways. It's been a long road for FAH to get to this point, but we are starting to see the possibility of seeing these results published easily before our 10th birthday (October 2010). Considering all the technology development that had to be done in the first five years, these results have come very quickly (in the last 3 years), which is exciting. In particular, we are now looking to apply these methods to other protein misfolding diseases (we have pilot projects for Huntington's Disease underway).

Finally, I should stress that while we're very excited about this, it's still early and a lot can go wrong between where we are and having a drug that doctors can prescribe. Over the holidays, we will be double checking the experimental data, crossing t's and dotting i's to make sure there is nothing missed before we think about submitting this for peer reviewed publication. Also, there is still a long way from an interesting possible drug (where we are now) to something which has passed FDA clinical trials (where we'd love to be), and a lot can go wrong in clinical trials in particular.

Thus, this is an important milestone for FAH and we are very grateful to all who have contributed. Happy holidays to all!

This is why we FOLD

[Soultribunal]

This is why I don't turn of my computer now.
Thanks HWC for letting me into the 'fold'.

I'll keep doing it until this computer decides to join my old computers!!

ST

[chrisk]

Hopefully some people will get some new gear over the holidays that will get us crunching some more ppd

[LCB001]

Originally Posted by chriskwarren

Hopefully some people will get some new gear over the holidays that will get us crunching some more ppd

Amen to that, I won't be getting anything new till spring, hoping to get an i7 and experiment with linux in a VM. The linux SMP with the a2 core is supposed to produce much higher PPD, one poster on the Folding forums was getting over 7700 ppd with HT and the -smp 8 flag.
What we need is to lure people like 3oh6 over to our team, twin 280's on a i7 board with 8 threads of WCG on the side, Wow!!...