Stanford’s Chemistry Department Research Highlights

Recently, for the first time, Stanford’s Chemistry Department did a look back at research highlights from the last (2013-2014) academic year done in the Department.  Folding@home is prominently highlighted:

https://chemistry.stanford.edu/events/chemistry-year-review

Stats update back on line

Over the weekend, we had an issue with one our key servers that handles the stats update.  The sysadmins have taken care of it and the stats update is now back on line.

Folding at the Chrome Browsers to Reveal the Secrets Behind the Type II Diabetes

In the past couple of years, Xuhui Huang’s group at HKUST
(http://compbio.ust.hk/) has performed large-scale molecular dynamics
simulations at Folding@Home (Project 2974-2975) to investigate the
mis-folding of the hIAPP (human islet amyloid polypeptide, also called
amylin).

Like other misfolding peptides, hIAPP is generally unstructured in
water solution but adopts an alpha-helix structure when binds to the
cellular membrane. Around 95% of patients with Type II diabetes
exhibit large deposits of misfolded hIAPP (beta-sheet fibrils).  The
aggregation of this peptide is suggested to induce apoptotic
cell-death in insulin-producing β-cells that may further cause the
development of the type II diabetes.  Using Markov state models
constructed from many molecular dynamics simulations, we have
identified the metastable conformational states of the hIAPP monomer
and the dynamics of transitioning between them.  We show that even
though the overall structure of the hIAPP peptide lacks a dominant
folded structure, there exist a large number of reasonably populated
metastable conformational states.  Among them, a few states containing
substantial amounts of β-hairpin secondary structure and extended
hydrophobic surfaces may further induce the nucleation of hIAPP
aggregation and eventually form the fibrils.  These results were
published at Qin, Bowman, and Huang,  J. Am. Chem. Soc., 135 (43),
16092–16101, (2013) (http://pubs.acs.org/doi/full/10.1021/ja403147m).

In 2014, our lab in collaboration with the Pande group at Stanford
University has successfully developed a new Folding@home client that
can run at the Chrome Web Browsers.  This new core is implemented on
Google Chrome’s Native Client (NaCl) platform (details here:
https://folding.stanford.edu/home/adding-a-completely-new-way-to-fold-directly-in-the-browser/).
Currently we have set up a NaCl folding server at Hong Kong
(folding5.ust.hk) to continue our study on the aggregation of the
hIAPP peptides.  Up to now, folding5.ust.hk has collected a few TBs
molecular dynamics simulation data of the hIAPP peptides.

We would like to thank all the donors for their generous
contributions!  We also welcome more clients to try out the new NaCl
Folding@home core.  If you are interested in this new core, you can
download it from the Chrome Store
(https://chrome.google.com/webstore/detail/foldinghome/hmnbjdgjgikbkapaolimfoidihobnofo).

 

Bowman lab moves to Washington University

I’ve been an independent researcher at UC Berkeley for the past three years and have now accepted an Assistant Professorship at Washington University in St Louis.  I’ll start the process of building a research team and our computing resources in the next few weeks, so I look forward to starting lots of new projects in the coming academic year!

Folding@home Next Steps Webinar Q&A

Last month Professor Pande gave a webinar/Q&A covering Folding@home’s next steps and accomplishments. Click on the link below to listen to and view the presentation-

http://on-demand.gputechconf.com/gtc/2014/webinar/gtc-express-folding-at-home-webinar.mp4

Bowman lab begins new vision projects

The Bowman lab is beginning a new effort to understand the molecular mechanisms underlying vision and the origins of inherited forms of blindness.  As a starting point, we’ve launched some new projects to understand the dynamics of rhodopsin. Rhodopsin is the protein responsible for detecting light in the eye and triggering a signaling cascade that ultimately results in an electrical stimulus that we perceive as an image. Rhodopsin functions by undergoing a conformational change in response to light. Importantly, mutations to rhodopsin can prevent it from having the desired dynamics, resulting in blindness. These projects will allow us to study the dynamics of rhodopsin, set a baseline for understanding the negative effects of such mutations, and potentially yield insight into therapeutic strategies for restoring or preventing vision loss.

Prof. Pande’s update on drug design successes with Folding@home

In the Stanford Big Data conference in 2014, I gave a talk which gives an update on our drug design efforts, summarizing a bit on how FAH works to design drugs and were we are in some areas (but not all — alas, it’s only a 12 minute talk, so I had to be pretty brief).  The talk is on the Stanford Big Data meeting web page:

http://bigdata.stanford.edu/advancing-drug-design-vijay-pande/

Folding@chrome – folding with just your browser

As those familiar with Folding@home (FAH) know, we’ve developed FAH to help simulate protein folding so that we can better understand how proteins get misfolded and cause diseases like Alzheimer’s, Mad Cow, Huntington’s, Parkinson’s, and many cancers. Better understanding protein misfolding allows designing drugs and therapies to combat these illnesses.

We have been working on ways to push FAH forward and have recently used a new technology provided by Google called Portable Native Client (PNaCl) to bring this folding application to the Web (via the Chrome browser ), so more people can contribute their computing power to solving this key problem.

For those interested in the technical details, Portable Native Client takes high-performance native code that uses a device’s full hardware capabilities and runs it in a browser tab, SIMD and threads included. PNaCl brings applications that need that extra computing power to the Web, and allows applications initially written for desktop (in C/C++ and making use of system interfaces like POSIX) to run in a browser. This is done portably, with support for x86-32, x86-64, ARM and MIPS on Windows, ChromeOS, Mac OS X and Linux.

In addition to making it easy for people to run Folding@home by simply going to this web page (with a Chrome browser), PNaCl also allows people to help FAH by embedding FAH+PNaCl into their own web pages, which would even further contribute computer power.   Our github page has instructions for how to do this.  Moreover, this NaCl client code is released with an open source license on github.

Folding@Home is supported by the NIH and NSF, and already has over 200,000 active users. It has been published in over 100 papers, including work in the prestigious journals Science and Nature. Please join us in finding the cure for these diseases, one laptop at a time, now with PNaCl support at http://folding.stanford.edu/nacl/

Webinar tomorrow — a chance for Q&A with Prof. Pande on Folding@home

Just a reminder of the webinar tomorrow.  I’ll present a brief summary of what FAH has done and where we’re going and then take questions.

This webinar is planned for June 3rd, 2014 at 9.00 AM Pacific Time.    If interested, please register ASAP at: http://bit.ly/FolHome

NaCl client points change

Due to concerns brought up by donors that the short work units of our NaCl Folding@home client may negatively impact the bonus point system (by allowing donors to cherry pick WUs and run NaCl fast WUs to bring up their completion rate), we’ve decided to eliminate bonuses for NaCl work units. The bonus point formula can yield disproportionately high points for fast computers running short work units. To compensate for this change we’ve increased base points to 125 for these work units. This should result in a much more fair PPD for NaCl clients.

Add your computer's power to over 327,000 others that are helping us find cures to Alzheimer's, Huntington's, Parkinson's and many cancers ...

... in just 5 minutes.

Step 1.

Download protein folding simulation software called

Folding@home

.

Step 2.

Run the installation. The software will automatically start up and open a web browser with your control panel.

Step 3.

Follow the instructions to Start Folding.

Stanford University

will send your computer a folding problem to solve. When your first job is completed, your computer will swap the results for a new job.

Download the protein folding simulation software that fits your machine.

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Installation guide