Project Status
To visualize the work of this project at the protein level, each protein is drawn below as a color dot on a 200x200 grid. The color indicates the status of each protein. Approximately 65,000 proteins are now being processed in this project. Enough work will go into the processing to generate 100,000 three dimensional structures for each protein.
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This image will be updated periodically.
News
Sep 15, 2009 - Most of our efforts in the fast few months have been spent trying out to tease more domains from the rice protein/proteome to increase the size of the project. These domains have been packaged into work units and are now crunching. So we have raised the number of protein structure predictions from roughly 40,000 initially to about 65,000 when all the larger sequences have been processed. Of these, we have roughly 35,000 completed so we still have about 30,000 to go (so it looks as though we're about halfway done now).
The logic and goal here is that the more comprehensive picture of the individual protein domains in rice we have, the more we can use that to inform us about the structures of other unknown domains in rice as well as other food crops. That is, partial information is much better than zero information. This enables us to obtain a better understanding of the pathways involved at atomic level detail.
Apr 8, 2009 - We have begun to analyze the protein models generated by Nutritious Rice for the World volunteers. The next step is to use sophisticated methods to select the top protein models for each gene. This will let us focus on a more manegable number of protein structures from the billions generated so far. Rice proteins are very different from what has been previously studied and only 1% of the proteins we're working on have segments which are significantly similar to proteins of known structure. That is why computer modeling is necessary and why this project is important. It also means that we have a lot of hard work ahead of us still!
In general, when proteins have similar amino acid sequences, they also have similar structures. The small number of cases where at least part of the protein sequence is similar to one where the structure is known are thus very useful. We have a good idea what those regions of the protein structure model should look like and this allows us to optimize and validate the tools that we use to pick the best models. That is what we are currently doing. Once we finish this, we will start processing the data and publish the best structures for each gene online.
Nov 12, 2008 - We continue to receive excellent results from you! Storing the predicted structures of 100 proteins requires about 10GB of bz2 compressed files. So far we have amassed over a terabyte of this data, and there's a lot more to be done. We are in the process of making room for storing this, and adjusting our clustering code to deal with this large number of results. Stay tuned for more as this develops.
The National Science Foundation, a significant source of funding for us, and World Community Grid separately interviewed us about our research and this project. Take a look!
In addition, we've modified the project status image above to reflect progress in the form of an animation. Each frame represents a moment in time when some significant number of workunits was submitted or results were returned. It gives you an idea for how things are moving along.
August 28, 2008 - Since the project began, you've sampled a space of about 3 billion potential structures for each protein and been credited for turning in the best ones. We've received structures for 6800 proteins so far -- that's over a billion structures. There are about 40,000 proteins to generate structures for, so we've got a while to go still!
While you continue to generate these structures, we'll be looking through them in more detail using clustering techniques. This will reveal to us those structures that resemble real proteins. We've applied this iterative process at smaller scales with success, and this larger pool of data for clustering will improve the accuracy of identifying good structure predictions.
And yes, the status image has been updated. :)
May 14, 2008 - The response to this project has been fantastic. Many people are excited and asking lots of good questions on the forums. We thank you all for an enthusiastic welcome to World Community Grid!
Our project has been mentioned in the press, which you can read about in the Press section of this site.
Finally, we've designed an image to keep you updated on the technical progress of this project.
May 12, 2008 - World Community Grid volunteers began processing the first work units of the project.
