1) Message boards : News : New publication: Our study of a disordered protein and its significance (Message 38749)
Posted 178 days ago by Profile nate
Badges updated! (Thanks to Toni)
2) Message boards : News : GPUGRID statistics graphs (Message 38747)
Posted 178 days ago by Profile nate
Nice! Looks really cool.
3) Message boards : Server and website : The "Performance" tab (Message 38743)
Posted 178 days ago by Profile nate
Thanks for letting us know. We'll look into it!
4) Message boards : News : New publication: Our study of a disordered protein and its significance (Message 38742)
Posted 178 days ago by Profile nate
Hi everyone,

We are very pleased to announce the publication of our latest research article, titled "Kinetic modulation of a disordered protein domain by phosphorylation", which was published yesterday in the journal Nature Communications. You can see the official journal page link here. Since we know most of you don't have access to the fancy formatted version from Nature Publishing Group, we have placed the our less-fancy formatted pre-print version of the article here (first PDF link at the top of the page).

Since I am sure the title and abstract is quite cryptic/confusing to everyone, let me explain what we discovered and why this work was important. The main focus of the paper was a disordered protein domain called KID. Disordered proteins like KID do not have any rigid structures (so no x-ray crystal structures), and are in fact very flexible like polymers. However, despite being flexible they are very important and common in many different aspects of cell biology. They are important in many protein-protein interactions, such as ones that are important in communication inside the cell. They are frequently involved in many diseases like cancer (among many others).

KID is a protein that has been studied for more than 15 years, and a lot was already known about it. Other proteins in the cell chemically modify KID through a process known as phosphorylation, which then causes it to bind to specific proteins. It binds most famously to a protein known as KIX. The behavior of KID in the phosphorylated and normal state has been studied by a technique known as NMR (a cousin of MRI), and the binding of KID to KIX has also been studied this way. However, what we discovered in our study—and not seen by any other method yet—was that when KID is phosphorylated, it undergoes an a slowdown in its motions and forms a temporary, partially folded state. We believe this state is important in the binding process, and modelling and comparison with previous experiments also suggest this. This work is significant because it is the first time anyone has shown that such chemical modifications could change the behavior of a protein in this way, and also that it could have important consequences for the way proteins interact.

If you have questions, please ask away. We will assign badges and update the webpage soon.
5) Message boards : Server and website : Upload Problems (Message 37680)
Posted 249 days ago by Profile nate
There is now plenty of space on the server so no one should be having upload/download problems. Of course, please let us know if any of you still has problems. We still have work to do to ensure this doesn't happen again, but that's for us to worry about.
6) Message boards : Number crunching : All WUs suddenly failing - output file absent (Message 37018)
Posted 322 days ago by Profile nate
FYI http://www.gpugrid.net/forum_thread.php?id=3770&nowrap=true#37017
7) Message boards : Number crunching : NOELIA WU (Message 37017)
Posted 322 days ago by Profile nate
Hello all.

The NOELIA_SH2eq workunits were all failing, so those have been cancelled.

There some other groups that follow the naming pattern NOELIA_TRPXXX. Those continue to run, because from what I can tell the ones that are being sent out now do not have a problem. The first post in this thread (http://www.gpugrid.net/forum_thread.php?id=3770&nowrap=true#36977) refers to a group that was cancelled, fixed and resent earlier in the week. However, if you continue to have problems with those please let me know here.

8) Message boards : Number crunching : CPU work units (Message 37007)
Posted 323 days ago by Profile nate
I believe there are some on the way right now. Stay tuned!
9) Message boards : Number crunching : NOELIA WU (Message 37006)
Posted 323 days ago by Profile nate
Hey guys,

We're looking into it. Unfortunately Noelia is away right now so we may have to cancel them for now. Thanks for catching it and pointing it out.

10) Message boards : News : WU: CMYBKIX (Message 36975)
Posted 329 days ago by Profile 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.


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