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Folding@Home Information

Stanford's goal: to understand protein folding, protein aggregation, and related diseases.



What are proteins and why do they "fold"? Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out their biochemical function, they remarkably assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, remains a mystery. Moreover, perhaps not surprisingly, when proteins do not fold correctly (i.e. "misfold"), there can be serious effects, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, and Parkinson's disease.

What does Folding@Home do? Folding@Home is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. Stanford uses novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. This has allowed us to simulate folding for the first time, and to now direct Stanford's approach to examine folding related disease.



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[H]ard|Folding News Articles
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Folding@Home
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,406,527
Work Units: 6,090

Posted: Fri Oct 29, 2010 04:29 pm
Folding@home has now been running for 10 years.

Quote:
Its with great pleasure that I announce that today is Folding@homes official tenth anniversary. Its been an amazing 10 years, especially in terms of what weve collectively been able to do, and my team and I are grateful for all the contributions by millions of people that has made this possible.


Full article: here

Happy Halloween everyone.
Misfolded Neural Proteins Linked to Autism Disorders
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,406,527
Work Units: 6,090

Posted: Mon Sep 27, 2010 02:28 pm
Stanford is "keeping our eye on this system for possible future FAH projects."

Quote:
An international team of scientists, led by researchers at the University of California, San Diego, has identified misfolding and other molecular anomalies in a key brain protein associated with autism spectrum disorders.


Full story here



Stanford also released 2 folding papers

Quote:
Recent work from detailed simulations of protein folding resulting from Folding@home have suggested some surprises and radical changes in how one conceptualizes protein folding kinetics. One of the more unusual aspects found in these simulations is the role of the native state as a kinetic hub (see paper #74). Here, we propose a new theory of protein folding that uses structural information in its kinetic equations and gives a much richer picture than previous theories. One key result is a prediction for what would cause the native state to be a kinetic hub and when one would see this effect (and in particular why it was not seen in simpler simulation studies previously.


Full article here


Quote:
By analyzing recent results from Folding@home, we have found a set of general properties emerging regarding how proteins fold. In particular, one of them comes as a surprise compared to previous models: the native state is a kinetic hub. This has implications for how we think about protein folding in general as well as applications of protein folding in biology and disease.


Full article here
Stanford releases Nvidia/Ati compatible Memtest
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,406,527
Work Units: 6,090

Posted: Tue Aug 24, 2010 10:51 pm
Stanford has released a utility called MemtestCL. This utility is compatible with both Nvidia and ATI based video cards.

Quote:
One of our concerns at Folding@home is the reliability of returned results - when you run on hundreds of thousands of machines around the world, in diverse environments, it's virtually guaranteed that some machines will be faulty. We've long advocated the use of reliability-verification tools to make sure your machine is working properly, especially for users who overclock their machines. While good utilities are available for this task on CPUs and system RAM (e.g., StressCPU and Memtest86), few tools are available for these tasks on GPUs because of their relative novelty.

Last year, we released the MemtestG80 GPU memory checker, an analog to Memtest86 for NVIDIA CUDA-enabled GPUs. This has been widely used by the community to catch misbehaving video cards. To bring this testing capability to a wider audience, we've just released a new, OpenCL-based GPU memory tester named MemtestCL. Because it's based on OpenCL, users of ATI video cards (Radeon 4000 series and newer) are now able to validate their GPU memory as well as users of Nvidia video cards. Both MemtestG80 (CUDA) and MemtestCL (OpenCL) implement the test patterns from Memtest86 (as well as a couple custom patterns) to make sure your GPU memory is working correctly.


Download here

GPU3 open beta test continuing well
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,406,527
Work Units: 6,090

Posted: Sun Jul 25, 2010 07:12 am
Stanford is continuing work on the gpu3 client and ati port.

Quote:
I wanted to post an update on our GPU3 beta test. It is going well, so we have put the GPU3 client on our high performance client download page. This new client is required for all Fermi hardware, but also allows pre-Fermi NVIDIA GPUs to access the new GPU3 cores. These cores are labeled core15 (which has already been extensively tested and is in production right now) as well as a new core16 which will be appearing in testing in the coming weeks.

We are also working to finish our OpenCL port for ATI GPUs to support GPU3 on ATI, but there are still performance issues for OpenCL on both NVIDIA and ATI which are holding back this release. You can see more information about the key software behind the GPU3 cores at the OpenMM project website. If you're curious, there is openCL code there for NVIDIA and ATI and we invite the open source OpenCL community to check out this code and see how they can help if interested (note the code is released under an LGPL license).


Improving Understanding Of Protein Folding
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,406,527
Work Units: 6,090

Posted: Fri Jun 25, 2010 09:48 am
Quote:
Physicists at UC Santa Barbara have created a microscopic device to assist biologists in making very fast molecular measurements that aid the understanding of protein folding. This development may help elucidate biological processes associated with diseases such as Alzheimer's and Parkinson's. Since proteins in the body perform different functions according to their shape, the folding process is considered a key area of study.


Full article here
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