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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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Folding Client 7.1.38 Released
King_N
[H]ard|Folding Administrator


Posts: 104
Points: 2,859,398
Work Units: 6,705

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: 104
Points: 2,859,398
Work Units: 6,705

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: 104
Points: 2,859,398
Work Units: 6,705

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
New protein structure model to inhibit cancer
King_N
[H]ard|Folding Administrator


Posts: 104
Points: 2,859,398
Work Units: 6,705

Posted: Sat Jul 30, 2011 07:20 am
Quote:
Researchers at the University of Hertfordshire have developed a new structural model of a protein, which makes it possible to develop more effective drugs to target diseases such as cancer, heart disease and influenza.


Full Article here

Also researchers have found that Age-related brain shrinking is unique to humans

Quote:
As we age, our brains get lighter. By 80, the average human brain has lost 15% of its original weight.

People suffering with age-related dementias, such as Alzheimer's, experience even more shrinkage.

This weight loss is associated with a decline in the delicate finger-like structures of neurons, and in the connections between them.


Full Article here
Folding V7 Beta Client Update Status
King_N
[H]ard|Folding Administrator


Posts: 104
Points: 2,859,398
Work Units: 6,705

Posted: Sun Jun 26, 2011 12:44 pm
Stanford has been working on the new v7.1.25 and v7.1.26 clients and have posted a status report.

Quote:
It's been a little while since our last v7 beta release (v7.1.24) and so I wanted to give donors some sense of what's going on. We've been working on internal testing of two releases past the current beta release and fixing bugs along the way. While we could in principle release v7.1.25 to open beta, there are enough todo items that we've decided to hold off a bit until it's a bit cleaner and further along. However, we're not going to hold off forever of course, just long enough for our developers to make some significant progress, especially since doing a release generates a lot of feedback, which takes developers away from coding.

To give some sense of where we are, here's the internal release notes for two recent builds (v7.1.25 and v7.1.26). Note that v7.1.26 is still in progress. Also, the #'s after the comment refer to our bug tracker. We have opened up the bug tracker, so one can see progress directly there on a daily basis if you're interested.



v7.1.26 (still under development):

* Failed upload attempt could cause WU to dump before it was expired. #679.

* Added AMD Radeon HD 6600 Series to GPU white-list.

* Fix failure to restart FAHControl in OSX when 'start minimized'. #649.

* Fixed a socket bug that could cause the loss of the end of a message.

* Build OSX client in 32-bit mode with Intel compiler.



v7.1.25:

* Hide 'Quit on window close' option in OSX.

* Fixed some problems with WU assign time and time offset calculations.

* Detect and ignore invalid assign time from older WS.

* Log computed WS time offset.

* Removed warning from Slot configuration about changing threads mid-run.

* Catch and log error accessing battery info in /sys on Linux

* Fix grayed out name and IP in client add after viewing local client. #640.

* Remove 'RS480 PCI-X Root Port' from GPU whitelist. #635

* Added a few new Radeon HD 6xxx cards.

* Added Nvidia GTX 590 device ID 0x1088 to whitelist.

* Increase Radeon HD 5xxxx and 6xxxx GPU type level by one. #653.

* Don't fail WS connections if all data was recieved even on net error.

* Print IP Address with 'Uploading' message.

* Fixes for OSX minimize and quit bugs. #649 & #659.

* Limit max CPUs per slot to system count. #652.

* Attempt to fix #654.

* Release system resources when querying OSX battery status. #650.

* Don't send 'auth' command from FAHControl if empty. #658.

* Fixed 'slot-add' NULL pointer exception. #666.

* Fixed 'log-updates start' error. #671.

* Fixed FAHClient script parsing bug. #676.

* Show 'Remote Access' tab in advanced mode. #648.

* Don't allow minimizing to sys-tray if it is not there. #670.

* Also print core return code numbers in hex. #677.

* Print times in ISO 8601 format. #664.

* Expire WUs in sending status.


Full Article here
  • Stickies: 0
  • News Articles: 159
  • Pages: 32
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