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DC Projects => [email protected] => Topic started by: PiNkY on June 05, 2006, 09:17:45 PM

Title: Folding News
Post by: PiNkY on June 05, 2006, 09:17:45 PM
From the [email protected] News Page (

6/6/2006 Update
We've had a busy few months preparing for some new roll outs. In particular, there has been a lot of progress on the GPU front and on some new results. Due to some NDAs (either from collaborating companies or journals, who don't want us to talk about work before it's published), it's a bit too early to go into details, but we've updated the high performance FAQ ( and the diseases FAQ (

Title: Re: Folding News
Post by: TLD on June 05, 2006, 09:30:35 PM
That has some good info PiNkY i was wondering about that BOINIC [email protected] client. :)

Title: Re: Folding News
Post by: PiNkY on June 05, 2006, 09:46:35 PM
yep, there's a little bit of info at the bottom of the "high performance faq" page linked above... :)

Title: Re: Folding News
Post by: TLD on June 06, 2006, 10:46:12 AM
Yes i was refering to that good info. :D

Title: Re: Folding News
Post by: PiNkY on July 03, 2006, 11:20:35 PM
more from the [email protected] news page:

[email protected] Principle Investigator Vijay Pande wins the Irving Sigal Young Investigator Award from the Protein Society.
From their web site ( "The Irving Sigal Young Investigator Award, sponsored by Merck Research Laboratories, recognizes a significant contribution to the study of proteins by a scientist who is in the early stages of an independent career and, generally, not more than 40 years of age at the time of the award. The 2006 awardee is Dr. Vijay Pande (Stanford University) for his unique approach to employing advances in algorithms that make optimal use of distributed computing, which places his efforts at the cutting edge of simulations. The results have stimulated a re-examination of the meaning of both ensemble and single-molecule measurements, making Dr. Pande’s efforts pioneering contributions to simulation methodology." Prof. Pande will accept the award at the Protein Society meeting in August and present the most recent results from [email protected] in his award lecture.

Stats server maintenance.
We are working on updating the stats server for v6. We will need to take the web interface to the stats down for several days. We will therefore not do this all at once, but starting Monday, we will have the stats update down a bit so our update can catch up. The actual stats will be updating, just the web interface for people to check their stats will be down.

Title: Re: Folding News
Post by: TLD on July 06, 2006, 11:02:14 PM
Anybody having a hard time getting FAH WUs over here, we have a couple peeps over at Crunchers Inc who keep having problems.

Title: Re: Folding News
Post by: PiNkY on July 06, 2006, 11:19:58 PM
nope, been running pretty smoothly for me... :)

Title: Re: Folding News
Post by: TLD on July 07, 2006, 02:48:39 AM
Big V was having problems and Rick isn't getting any WUs now.

Title: Re: Folding News
Post by: PiNkY on July 07, 2006, 02:56:47 AM
it's possible the server they need to connect to is down, although i think it's supposed to hold onto the unit it's attempting to submit, and download a unit from a different server if it runs into that problem. :think:  here's ( the server status page, you can find out which server you're attempting to connect to in the fah log files, if i recall correctly...or look up the unit and it should give you a server ip.

Title: Re: Folding News
Post by: fingerle on July 07, 2006, 06:24:24 AM
Only problem I've been having is the occasional "Can not connect to assignment server(results)" message come up.
Minor annoyance factor. Job just sits in the queue for a bit till the connection is made.

I say annoyance factor cause upon check of the server status page, it's always listed as online.  ???
Haven't seen any of my rigs without work tho. 8)

Title: Re: Folding News
Post by: PiNkY on July 14, 2006, 02:35:21 AM
From the [email protected] news page:

Major new result
We have a significant new result which just came out today in Science magazine. See the papers ( page for more details (it's also significant as this marks the fortieth paper for FAH!).

From the papers page:

Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory (
Ian T. Suydam, Christopher D. Snow, Vijay S. Pande, Steven G. Boxer.
Science (2006)

SUMMARY: The ability to quantitatively predict electric fields in proteins has remained a great challenge. In this paper, we combine new experimental methods with new theoretical methods made possible by [email protected] distributed computing to greatly push the boundary of what one could previously predict. In particular, we see that a single structure is insufficient to make accurate predictions, suggesting that the ensemble approaches inherent to [email protected] may be important in predicting electrostatics in proteins.

ABSTRACT: The electric fields produced in folded proteins influence nearly every aspect of protein function. We present a vibrational spectroscopy technique that measures changes in electric field at a specific site of a protein as shifts in frequency (Stark shifts) of a calibrated nitrile vibration. A nitrile-containing inhibitor is used to deliver a unique probe vibration to the active site of human aldose reductase, and the response of the nitrile stretch frequency is measured for a series of mutations in the enzyme active site. These shifts yield quantitative information on electric fields that can be directly compared with electrostatics calculations. We show that extensive molecular dynamics simulations and ensemble averaging are required to reproduce the observed changes in field.

Title: Re: Folding News
Post by: PiNkY on July 14, 2006, 02:36:22 AM
not sure what that means overall, though it's nice to see work being put to use and reported on :D

Title: Re: Folding News
Post by: TLD on July 14, 2006, 09:05:08 AM
Wow thats a mouth full, as you say good to see our work being used. :thumb:

Title: Re: Folding News
Post by: PiNkY on July 19, 2006, 03:53:18 AM
in case anyone was seeing hiccups yesterday, it was probably due to [email protected]'s server move.  was wondering why the noon stats run for my sig image didn't go through, and eoc stats didn't update... :doh:  sounds like it was mainly stats servers affected...  also, if you have an address that starts with vspx27 bookmarked, that part of the address should be changed to fah-web now.

Title: Re: Folding News
Post by: PiNkY on July 24, 2006, 08:40:53 PM
they really need to either speed up folding forum, and maybe then i'd check it a bit more often and find out that something's happening....either that, or put an rss news feed out or something. :doh:

anywho....over the weekend, the heat was bad enough that they had trouble cooling the server room - which resulted in them turning off a few servers.  if you couldn't return results over the weekend, that may have been the cause.  they're slowly working on bringing the servers back up, now. :)