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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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Protein folding and viral infection
King_N
[H]ard|Folding Administrator


Posts: 98
Points: 2,738,192
Work Units: 6,434

Posted: Mon Feb 27, 2012 02:00 am
Stanford has released a few new articles.

Protein folding and viral infection

Quote:
Understanding protein folding has many possible areas of biological and biomedical impact. For example, consider one of the major research areas of the Kasson lab at the University of Virginia, namely how the influenza virus infects cells. In the past, Dr. Kasson and Dr. Pande have studied two aspects of this: how the influenza virus recognizes cell-surface receptors so it infects the "right" cell types and how small vesicles fuse.


Dr. Kasson's group is now looking at the function of the viral protein that controls cell entry, a protein called hemagglutinin. The hemagglutinin protein interacts with cell membranes: one piece inserts into the membrane, refolds, and alters the membrane in some unknown manner to promote viral entry. Another piece links the viral and cell membranes and refolds to bring the two together. We are running simulations on Folding@Home to examine each of these pieces. Dr. Kasson's laboratory also looks at these processes experimentally.


Full Article here.


Protein Folding and Molecular Recognition

Quote:
In the past a couple of years, the FAH has greatly helped us on our research on understanding the mechanisms of the molecular recognition processes. Molecular recognition, such as enzymes need to recognize their substrates and drugs have to be designed to specifically bind to certain receptors, is crucial to biology and medicine. Experimentally probing the chemical details of molecular recognition events is challenging, while computer simulations have the potential to provide a detailed picture of such events. With the help of the FAH donors, we are performing large-scale simulations on a group of Periplasmic Binding Proteins aiming to reveal the general relationships between protein structures, its intrinsic dynamics, and mechanism of recognition process.


Full Article here.


LTMD: Key new technology for accelerating folding and misfolding simulations in FAH


Quote:
The Izaguirre Lab at the University of Notre Dame (http://www.nd.edu/~lcls) has been collaborating with the Pande Lab at Notre Dame to produce a new GPU core that leverages the amazing speed of OpenMM implicit-solvent force calculations (the heart of the GPU core in Folding@home) with new Long Timestep Molecular Dynamics (LTMD). This combination currently allows nearly a 10-fold speedup over OpenMM for systems as small as the WW domain (35 residues, 544 atoms) up to the Lambda repressor (80 residues, 2000 atoms). This translates into about 10 microseconds per day of simulation, which brings single trajectory millisecond simulations closer to FAH.

In collaboration with Cauldron Development (lead by Joseph Coffland, primary developer of the Folding@home client and also some cores), we hope to produce a GPU core that might be the first hybrid CPU-GPU core. There are technical questions on how to best do this, and we will engage our enthusiastic beta-tester GPU donors to discuss how to best approach this core when we are closer to production mode.


Full Article here.

Protein In The Brain Could Be A Key Target In Controlling Alzheimer's
King_N
[H]ard|Folding Administrator


Posts: 98
Points: 2,738,192
Work Units: 6,434

Posted: Sun Jan 29, 2012 06:43 pm
This has been a relatively quiet month, there has been no new news released by the Stanford folding team, so there is not much I can report.

However I did run across this interesting Alzheimer's news article.

Quote:
A protein recently discovered in the brain could play a key role in regulating the creation of amyloid beta, the major component of plaques implicated in the development of Alzheimer's disease, according to researchers at Temple University's School of Medicine.

A group led by Domenico Pratico, professor of pharmacology and microbiology and immunology at Temple, discovered the presence of the protein, called 12/15-Lipoxygenase, in the brain three years ago.

"We found this protein to be very active in the brains of people who have Alzheimer's disease," said Pratico. "But three years ago, we didn't know the role it played in the development of the disease."

Following two years of study, the Temple researchers have found that the protein is at the top of a pathway and controls a biochemical chain reaction that begins the development of Alzheimer's.


Full Article here
Multiple Myeloma First Risk Genes Discovered
King_N
[H]ard|Folding Administrator


Posts: 98
Points: 2,738,192
Work Units: 6,434

Posted: Thu Dec 29, 2011 07:55 pm
It's been a rather slow month for news.

Stanford has finished their stats re-credit, they ask that you let them know if there is still problems.


On the cancer news front

Quote:
According to a paper published online in Nature Genetics, a team of scientists led by The Institute of Cancer Research (ICR) has demonstrated for the first time that a person's genes influence their risk of developing multiple myeloma, a cancer of plasma cells, which is a type of white blood cell responsible for the production of antibodies.


Full Article here


Also there was a slight problem with the database earlier this month, the site was down for a short time while the issue was dealt with. Everything appears to be back to normal.

Recent video about Folding@home from the Stanford News Service
King_N
[H]ard|Folding Administrator


Posts: 98
Points: 2,738,192
Work Units: 6,434

Posted: Sat Nov 26, 2011 05:25 pm
Stanford has released a video about Folding.



View Video here


Also Stanford has made changes to the "Big Advanced Projects" which will go into effect Jan 16th.


Quote:

Big Advanced (BA) is an experimental type of Folding@home WUs intended for the most powerful machines in FAH. However, as time goes on, technology advances, and the characteristics associated with the most powerful machines changes. Due to these advances in hardware capabilities, we will need to periodically change the BA minimum requirements. Thus, we are shortening the deadlines of the BA projects. As a result, assignments will have a 16 core minimum. To give donors some advance warning, we are announcing this now, but the change will take place in 2 months: no earlier than on Monday January 16, 2012.

We understand that any changes to how FAH works is a disruption for donors, and we have been trying to minimize such changes. For that reason, we are not changing the points system at this time.

However, we want to emphasize that the BA program is experimental and that donors should expect changes in the future, potentially without a lot of notice (although we will try our best to give as much notice as we can). In particular, as hardware evolves, it is expected that we will need to change the nature of the BA WUs again in the future.
Folding Client 7.1.38 Released
King_N
[H]ard|Folding Administrator


Posts: 98
Points: 2,738,192
Work Units: 6,434

Posted: Tue Oct 25, 2011 03:05 pm
A New Folding Client has been released, v7.1.38

Changelog for the last few updates is below.

Quote:
v7.1.38:
Fixed network connection dropping.


v7.1.37:
Added missing wraplabel.py file to FAHControl.
Changed socket error message verbosity.
Fail WU on UNSTABLE_MACHINE immediately & return for partial credit. #615


v7.1.36:
Fixed a potential socket connection bug. Maybe related to #734.
Added several NVidia cards to GPUs.txt. #737.
Improved Linux on battery detection. #738.
Print WU error state on WU status line.
Emit correct exception on FAH transaction failure. #615.
Fixed debian package install core permissions problem. #732.
Removed core byte order warning. #602.
Added GPL link to FAHControl about. #736.
Ask user, team, passkey and mode during .deb package install. #739.


v7.1.35:
Added 'Enchanter' theme. #731
Renamed 'Wimp' to 'Windows-Default'. #731
Unminimize FAHControl window on unhide. #567
Better core download failure message. #161
Cleaned up project descriptions using html2text.py.
Store project data in client DB.
Use system default font size. #733
Added project info to viewer. #575.
Added clickable buttons to viewer.
Fixed FAHViewer crash introduced in v7.1.34.
Fixed mouse wheel scrolling in FAHControl. #463.
Fixed color difference for text boxes. #698.
Changed FAHControl window name. #711.


v7.1.34:
Fixed CPU consumption in client connections. #702
Really fixed "Wrong architecture" bug on 32-bit Ubuntu. #599
Only warn on config errors. #722
Log error and continue of command server fails to initialize.
Fixed Slot configuration text. #717
Use -1 or 0 for CPUs default to be consistent with GPU options. #717
Disabled no longer supported AMD X1300 - 1900 GPUs.
Added "OpenGL Render" to info in FAHViewer. (For blacklisting)
Added 'override-blacklist' option to FAHViewer. (Nothing black listed yet)
'OK' -> 'Save' in FAHViewer preferences window. #724
Fixed NVIDIA_DEV.1244.01 = "NVIDIA GeForce GTX 550 Ti" detection.
Added the 'Wimp' theme and win32 theme engines. #723
Made 'Wimp' theme the default in Windows. #713
Added heartbeat to viewer<->client connection to timeouts dead connections.
Stop trying FAILED, FAULTY and DUMP reports if WS connection was made. #728
Check WS server versions for unreasonable values. #728.


Client Download: here



Stanford also released a paper showing the Comparison between FAH and Anton's approaches.

Quote:
Right now, the two most powerful supercomputers for studying protein folding are Folding@home and a very impressive special purpose computer from DE Shaw Researched, called ANTON. We're often been asked "how do they compare?" The approaches are very different, so comparisons aren't completely straightforward. ANTON takes the traditional approach to studying protein folding, where one performs a few (often 1 or 2) long trajectories to study the process. Folding@home takes a statistical approach, which has two primary benefits: 1) it can access folding on dramatically longer timescales (milliseconds, instead of microsecond folding events over a single long trajectory) and 2) it can give statistically significant results on those long timescales.

The main concern about the method in FAH is that since it is such a radically new approach, does it work reliably? Previous tests of FAH have been to experiment, which is the gold standard test, but also brings in other issues, such as how good are our models of reality. Thus, while FAH's approach has done well compared to experiment, it is useful to compare FAH and ANTON directly, since they use the same models, etc. Comparison of our statistical approach (using Markov State Models, aka MSMs) directly with data from ANTON would go a long way to showing that the MSM approach works for even non-trivial systems (they have been previously tested for long dynamics on small systems).


Full Article: here


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