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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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  • Stickies: 0
  • News Articles: 156
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Multiple Myeloma First Risk Genes Discovered
King_N
[H]ard|Folding Administrator


Posts: 101
Points: 2,811,473
Work Units: 6,593

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: 101
Points: 2,811,473
Work Units: 6,593

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: 101
Points: 2,811,473
Work Units: 6,593

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


Award-winning research points toward Alzheimers vaccine
King_N
[H]ard|Folding Administrator


Posts: 101
Points: 2,811,473
Work Units: 6,593

Posted: Wed Sep 28, 2011 06:46 pm
There really hasn't been any new news from Stanford this month, however I did run across this article dealing with research that could possibly lead to an Alzheimer's vaccine.

Quote:
AUGUSTA, Ga. An accomplice to the protein that causes plaque buildup in Alzheimers disease is the focus of a potential new treatment, according to research by a Georgia Health Sciences University graduate student.

In Alzheimers, the amyloid protein can accumulate in the brain instead of being eliminated by the bodys natural defenses, nestling between the neurons and forming impassable plaques.

Amyloid and the way it gets there could be targets for a new vaccine.


Full article here.
New Futures In Biotech episode about Folding@home
King_N
[H]ard|Folding Administrator


Posts: 101
Points: 2,811,473
Work Units: 6,593

Posted: Sat Aug 27, 2011 05:33 am
Vijay was a guest on the Twit Netcast, you can watch the interview here.

Also Vijay announced he just recieved the 2012 Michael and Kate Bárány Award.

Quote:
I have some good news. Due in large part to the work we've done with Folding@home, I've been named the recipient of the 2012 Michael and Kate Bárány Award for Young Investigators from the Biophysical Society for "developing field-defining and field-changing computational methods to produce leading theoretical models for protein and RNA folding." This was just annouced in the Biophysics Society newsletter and their web site hasn't been updated just yet for the 2012 awards.


Stanford also released a new paper this month.

Quote:
One major result is in the area of Alzheimer's Disease (paper #95). It is believed that Alzheimer's Disease results from the misfolding of the Abeta peptide. Understanding how Abeta misfolds could give us some key insights into how to cure Alzheimer's Disease. This paper experimentally tests a key prediction made in an earlier paper (paper #58: "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). In this paper, we show experimentally that there appears to be a beta turn in the Abeta as predicted. This leads to a very stable form of misfolded Abeta which could be used as a starting point for a new Alzheimer's therapy. We are heavily pursuing this research direction at the moment.


You may view the paper here
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