Hello WCG volunteers today I report yet another status report. We’re at over 80% completion and plan to begin preparing the manuscript that will describe the results by mid September. Here is the graphic describing the progress, nicely supplied by IBM.

http://www.worldcommunitygrid.org/images/rbonneau/HPFStatus200508242z2i5p6a.jpg



What will the results look like? They will be in a database accessible to all free of charge and will also have an interactive http interface that will look a lot like the one that we have for the Rosetta server (I think, we still have to work details out). For a peak of what integrated domain and structure prediction looks like see:

http://robetta.bakerlab.org/results.jsp?id=4822&p=14
http://robetta.bakerlab.org/results.jsp?id=4705&p=21

Some key differences are that the results from HPF will be precomputed so: no waiting and whole genomes are there. The Robetta server only allows people to submit small numbers of sequences at a time, so having whole genomes done by HPF is a critical step in getting people access to folding results. Another key difference is that the integration with other info about proteins will be better handled. [ Lars Malmstroem and Mike Riffle are key people working on this. ]

Well also have a graphical front end via Cytoscape ( www.cytoscape.org ) that is being developed here at the ISB by Iliana Avila-Campillo and Jungwahn Park. Since fold does not always trivialy equate to function (it rarely does ) we will provide functional association networks for all genomes folded as part of this project. Biologists can explore the function/fold data generated by HPF in the context of these networks (metabolic, operons, phylogenetic pathways, protein-protein interactions, etc). We want to give people a lot of different options for using/exploring the results of this project and this graphical front end is one of them.

Lastly, there is the possibility of extending this project with a second phase. The second phase (HPF2) would take important proteins with interesting novel predictions from HPF1 and refine those predicted structures (with something we call all-atom mode) to a higher level of resolution/accuracy (HPF1 == fold resolution, broad fold-function survey; HPF2 == higher res for more detailed conclusions). I’ll talk more about this next month.

Hit me with some questions!