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WCG Status Update

WCG Post

HPF 2 progress Report February 2006

There are a few things to report this month. If you have any questions about this stuff put the questions up as a post on the forum and we'll try to answer them soon.

News item #1:

We've posted some results (just some pictures of proteins from HPF2) for all you volunteers to check out. We've tested and retested the code and the resulting proteins and we can officially say that the beginning is over for HPF2 and now we're in the "extended crunching" stage...somewhere after mile 1 and somewhere well before mile 26.



Check these picture of HPF2 structures out again... The discerning eye will notice something fishy about these pictures, guess what is wrong (think about the difference between HPF1 and HPF2). So this is sort of a pop quiz. Check out the pictures and then see if you can guess what is missing...

Answer

News item #2:

We have received proteins from our collaborators in Seattle working on pregnancy malaria. These proteins are proteins that Patrick Duffy's lab has identified as possibly important in this particularly bad type of malaria (Plasmodium). Paul Shannon is one of the Bioinformatics scientists working with us on this project, he's looked for proteins that are: 1. The right size or have pieces/ domains the right size for Rosetta 2. Are unregulated/over-expressed during the type of malaria they study in Duffy's lab and 3. Not easy to annotate with other methods (unknown proteins). For more info on this lab's overall effort follow this link (where the need to look at these proteins was brought to our attention see: http://www.sbri.org/research/duffy.asp . Each time we look at a new set of proteins I'll try to put up an update. Before this we were looking at proteins from the Key organisms for this study, but this new set jumps the queue, as they are directly relevant to this research group. For a reminder of the three main disease related sets of proteins we will be crunching on this project see: http://homepages.nyu.edu/~rb133/wcg/thread_9681.html

Extra news item:

We have published another paper based off the HPF results. This paper will appear soon in PLoS biology. I'll let you know as soon as we have a web-express type link. The copy-editing phase has another week or two to go. In any case Lars Malmstrom. Mike Riffle, Dave Baker and I are happy to be done with the writing. The data is available via a web portal that Mike and Lars made that also serves up lots of other data-types from the UW yeast resource center. We're also happy that we can continue on to the next paper, focusing on the next release of the data. We'll start writing this next paper asap. In any case more on this next paper (in a chain of papers directly resulting from HPF1 & 2) when I have a link!

Goodnight for now, And thanks for crunching.