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Message boards :
News :
WU: CMYBKIX
(Message 36975)
Posted 3610 days ago by  nate
Hi all, I have submitted a bunch of new workunits to the short queue. This should fix the dry spell we have had there for the past week. The workunits are named "NATHAN_CMYBKIX". In these simulations I am investigating the binding of a small disodered protein named cMyb to another protein named KIX. Disordered proteins and disordered domains (as opposed to nicely structured ones like hemoglobin) are very important in protein-protein interactions. Mutations in disordered proteins are very common in cancers, amyloid fibril diseases like alzheimer's and parkinson's, and probably a lot of other disease we don't know about. So, with these simulations we will be taking some first steps towards understanding some key things about these types of interactions. Lessons we learn from this system should help us work on many, many others. Nate |
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Message boards :
Server and website :
No cpu tasks?
(Message 35906)
Posted 3676 days ago by nate
Strange. We have a lot of workunits in the line-up, so there shouldn't be an issue. We'll look into it. |
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13)
Message boards :
News :
WU: CMYB_equil
(Message 35905)
Posted 3676 days ago by nate
Those were the corrected ones. There is currently a CMYB_equil3 batch as well, that also seems to be going without problems. These simulations are part of a much bigger batch that will come soon. |
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14)
Message boards :
News :
WU: CMYB_equil
(Message 35853)
Posted 3678 days ago by nate
And indeed there was a problem, so I have stopped them and I will resend them corrected. Sorry about that. For some reason checks before submission did not flag the problem. Very frustrating. |
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15)
Message boards :
News :
WU: CMYB_equil
(Message 35850)
Posted 3678 days ago by nate
Hello all, I have submitted some simulations of a small peptide to the short queue. This is a special type of simulation, and it is also the first time I am running them, so there may be errors with them. Please let us know what you see. There should be pass through quickly, however, so hopefully they don't cause too many problems. Nate |
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16)
Message boards :
News :
Uncovering the role of membrane lipids in modulating enzyme activity
(Message 35000)
Posted 3718 days ago by nate
Hello everyone, At the end of last year, we updated the badge system to include several new publications we had just published. Today we want to highlight one of those pieces of work. Starting in Mid-2011 (an eternity ago), we began collaborating with a research group in Italy to better understand something strange they had been seeing in their experiments. Specifically, they were seeing that when they modified the composition of lipids in a cell membrane, the activity of an enzyme named FAAH increased. They came to us to try to better understand why that was happening. Through simulations performed here on GPUGRID we discovered that, contrary to expectations, the lipids modified the function of the enzyme by directly interacting with it and its endogenous ligand. It had been expected that structural changes in the membrane would be the culprit, but that was not the case. Additionally, we report the first unbiased binding of a lipid to a membrane protein. This is one of the first experiments of this kind ever performed, and was possible only because of the compute power we have here at GPUGRID. You can read more about it on the science page here, as well as check out the video of the binding event. Please note that (almost) all the papers we publish are available on our lab webpage. They can be found here. The versions of the documents there are the pre-print versions, basically meaning they are not formatted to look pretty. This is due to restrictions placed on us by the publishing companies. The text and figures are identical to those in the "pretty" version published in the journal, however. We are working on putting out copies of any papers missing from that page. Lastly, we remind you that GPUGRID accepts donations beyond compute time, and if you're interested you can see how to do so on our Donations page. Of course, the crunching time donated by all of you is greatly appreciated. Thanks and onward, The GPUGRID Team |
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Message boards :
Server and website :
New publications - one link not working
(Message 33957)
Posted 3801 days ago by nate
Yes, it will be officially published in two weeks, but it has been fully accepted and we are just working with the publisher on final formatting for the article. |
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18)
Message boards :
News :
New Badges for four new articles
(Message 33955)
Posted 3801 days ago by nate
Hi everyone, As some of you may have already noticed, we have updated the badges to include four recent publications. In other words, many of you should have new colored water badges with rankings in your profiles. In the coming days/weeks we'll be updating the Science pages with details about the new publications, as well as posting here and on the Facebook page to give you all some background about the works. If you have not received any badges in this round, please note that many of the workunits for this round were performed 1-2 years ago (inlcuding my infamous NATHAN_FAAH workunits, started in September 2011!). These papers have been a long time coming, and we are very glad to finally have the results published. Do not worry if you were not included in this round, because we expect to have another update in the coming months. Lots of good results in the pipeline, we are just trying to get them published. Finally, just a reminder that GPUGRID accepts donations beyond compute time, and if you're interested you can see how to do so on our Donations page. Of course, the crunching time donated is greatly appreciated. And as always, thanks and onward. The GPUGRID Team |
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19)
Message boards :
News :
WU: NATHAN_benfix
(Message 33682)
Posted 3823 days ago by nate
Hey guys, Minor group of workunits here on long queue. Just a small fix/check on some work we have sent for publication. You should barely notice them, and they should finish quickly. Regards, Nate |
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20)
Message boards :
News :
WU: FXArep
(Message 33505)
Posted 3838 days ago by nate
Some NOELIA WUs should start to trickle in now. There was an issue with the priority of certain tasks in the scheduler. Fixed now. |
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