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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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 DanielGordon04/16/14 
 Huberthans04/15/14 
 Voxelot04/11/14 
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2 new research articles released
King_N
[H]ard|Folding Administrator


Posts: 98
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Posted: Sat Nov 27, 2010 03:39 pm
Stanford has released 2 new research articles.

Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins

Quote:
Multiple variants of the AMBER all-atom force field were quantitatively evaluated with respect to their ability to accurately characterize helix-coil equilibria in explicit solvent simulations. Using a global distributed computing network, absolute conformational convergence was achieved for large ensembles of the capped A21 and Fs helical peptides. Further assessment of these AMBER variants was conducted via simulations of a flexible 164-residue five-helix-bundle protein, apolipophorin-III, on the 100 ns timescale. Of the contemporary potentials that had not been assessed previously, the AMBER-99SB force field showed significant helix-destabilizing tendencies, with beta bridge formation occurring in helical peptides, and unfolding of apolipophorin-III occurring on the tens of nanoseconds timescale. The AMBER-03 force field, while showing adequate helical propensities for both peptides and stabilizing apolipophorin-III, (i) predicts an unexpected decrease in helicity with ALA to ARG+ substitution, (ii) lacks experimentally observed 3-10 helical content, and (iii) deviates strongly from average apolipophorin-III NMR structural properties. As is observed for AMBER-99SB, AMBER-03 significantly overweighs the contribution of extended and polyproline backbone configurations to the conformational equilibrium. In contrast, the AMBER-99phi force field, which was previously shown to best reproduce experimental measurements of the helix-coil transition in model helical peptides, adequately stabilizes apolipophorin-III and yields both an average gyration radius and polar solvent exposed surface area that are in excellent agreement with the NMR ensemble.


Full article here


Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics

Quote:
Conformational equilibrium within the ubiquitous GNRA tetraloop motif was simulated at the ensemble level, including 10,000 independent all atom molecular dynamics trajectories totaling over 110 microseconds of simulation time. This robust sampling reveals a highly dynamic structure comprised of 15 conformational microstates. We assemble a Markov model that includes transitions ranging from the nanosecond to microsecond timescales and is dominated by six key loop conformations that contribute to fluctuations around the native state. Mining of the Protein Data Bank provides an abundance of structures in which GNRA tetraloops participate in tertiary contact formation. Most predominantly observed in the experimental data are interactions of the native loop structure within the minor groove of adjacent helical regions. Additionally, a second trend is observed in which the tetraloop assumes non-native conformations while participating in multiple tertiary contacts, in some cases involving multiple possible loop conformations. This tetraloop flexibility can act to counterbalance the energetic penalty associated with assuming non-native loop structures in forming tertiary contacts. The GNRA motif has thus evolved not only to readily participate in simple tertiary interactions involving native loop structure, but also to easily adapt tetraloop secondary conformation in order to participate in larger, more complex tertiary interactions.


Full article here

Folding@Home
King_N
[H]ard|Folding Administrator


Posts: 98
Points: 2,736,559
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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: 98
Points: 2,736,559
Work Units: 6,433

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: 98
Points: 2,736,559
Work Units: 6,433

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: 98
Points: 2,736,559
Work Units: 6,433

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).


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