Folding@home

New paper #62: The predicted structure of the headpiece of the Huntingtin protein and its implications for Huntington's Disease

It's still early (since this paper was just accepted), but I wanted to give FAH donors a heads up on our work on Huntington's Disease aggregation, which is just about to come out in the Journal of Molecular Biology.  I'll comment on it more in a future post.

See our papers page for more details.

AS code change

We've made a code change in the two main assignment servers (assign.stanford.edu & assign2.stanford.edu -- but no the PS3 or GPU AS's) to handle a potential problem people have been having with getting through firewalls.  

For those who are very experienced with running FAH (eg are familiar with the logs and how to interpret them):  If you have had problems in the past with your firewall, could you now try again and see if you can get a server assignment?  You likely won't be able to get to the server itself (we've just updated the AS code), but just knowing that this fix helped will let me know what we should update all of the work servers ASAP.

If everything was working fine, but now it isn't, please make a post in the forum:  http://foldingforum.org

Folding@home talk at PARC today, 4pm

Today (January 8, 2008) at 4pm, I'll be giving a talk at PARC, giving an update about Folding@home.  If anyone is local to the Palo Alto area, you can be there in person.  Note that they also do live streaming and should have a video on line (check out http://www.parc.com/forum for details).

UPDATE:  The talk can be found here:

http://www.parc.com/cms/get_article.php?id=799

OpenMM workshop -- @ Stanford Feb 12, 13

I've talked about OpenMM before -- it's the library we're releasing to allow other scientists to take advantage of the great speed up found in our GPU code.  We're now having a workshop to describe it.  Here is the announcement that went out (see below).  Check out this link for more details.

Want to learn how to quickly set up and run molecular dynamics (MD) simulations? Or are you a veteran to MD who wants to know how to obtain 100X speedups of MD code on GPUs? 

Whatever your MD background, the free upcoming two-day OpenMM workshop promises to be an exciting, knowledge-filled opportunity, featuring experts from both molecular dynamics and the GPU industry. 

Day 1 of the workshop is geared towards MD developers and will discuss how MD code can be sped up on GPUs and in particular, with the new OpenMM 1.0 library. Day 2 of the workshop is for researchers interested in using MD in their research, introducing MD theory and the new OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. You can sign up for one or both days. 

Read more about OpenMM, OpenMM Zephyr, and molecular dynamics (see attached). Or visit http://simbios.stanford.edu/EventsOfInterest/OpenMMWorkshop.htm for more details.

Updates to the stats system

We have made some updates to the stats code to make it faster and more useful.  The recent changes speed web page creation in general and also cache team pages such that they can be read during stats updates.  This is the first stage of further improvements of the stats to come in 2009.

new stats update schedule

We have switched the stats (points) update to occur every 3 hours instead of every 2 hours.  The reasoning here is that it takes about an hour to update the stats, and so doing this every 2 hours means that the stats are accessible only 1 out of every 2 hours.  However, doing the stats update every 3 hours doesn't take that much longer to update the stats (1 hour and 15 minutes vs 1 hour) and so this should make the stats more available.  The reason it doesn't take that much longer is that the stats update is done in batches by project to help db thrashing in and out of memory and so once a project db is in memory, it doesn't hurt to push through more stats.

We're going to try out this new schedule to see if this bears out.  If not, we'll go back to the old schedule.

New paper #61: Computational screen to identify important mutations in influenza

We're happy to announce a new Pande Group paper (paper #61 at http://folding.stanford.edu/English/Papers).  This paper describes a new computational screen to identify important mutations in influenza:

Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin. 
Peter M. Kasson and Vijay S. Pande. Pacific Symposium on Biocomputing 14:492-503(2009). 
Download URL: http://psb.stanford.edu/psb-online/proceedings/psb09/kasson.pdf  

The influenza hemagglutinin protein performs several important functions, including attaching the virus to cells it will infect and releasing the viral genome into the interior of the cell. Most protective antibodies against influenza also bind to the hemagglutinin protein. We wish to understand how mutations to hemagglutinin affect viral function, including what keeps avian influenza ("bird flu") from being readily transmissible between humans. In this paper, we have applied a technique from information theory known as mutual information to genetic sequence data to predict important mutation sites on the hemagglutinin protein. In follow-up work, we are combining this technique with other methods to refine these predictions and test some of them using Folding@Home. 

PS For those curious out in more details, check out the paper (see link above) or the technical abstract:

Influenza hemagglutinin mediates both cell-surface binding and cell entry by the virus. Mutations to hemagglutinin are thus critical in determining host species specificity and viral infectivity. Previous approaches have primarily considered point mutations and sequence conservation; here we develop a complementary approach using mutual information to examine concerted mutations. For hemagglutinin, several overlapping selective pressures can cause such concerted mutations, including the host immune response, ligand recognition and host specificity, and functional requirements for pH-induced activation and membrane fusion. Using sequence mutual information as a metric, we extracted clusters of concerted mutation sites and analyzed them in the context of crystallographic data. Comparison of influenza isolates from two subtypes—human H3N2 strains and human and avian H5N1 strains—yielded substantial differences in spatial localization of the clustered residues. We hypothesize that the clusters on the globular head of H3N2 hemagglutinin may relate to antibody recognition (as many protective antibodies are known to bind in that region), while the clusters in common to H3N2 and H5N1 hemagglutinin may indicate shared functional roles. We propose that these shared sites may be particularly fruitful for mutagenesis studies in understanding the infectivity of this common human pathogen. The combination of sequence mutual information and structural analysis thus helps generate novel functional hypotheses that would not be apparent via either method alone.