Hi Tom --
Thanks for bringing this to the forums. I found a similar information in a bulletin published on the web by BioIT at http://www.bio-itworld.com/news/041805_report8136.html. My understanding of this will be quite simplistic because I am not a computational research scientist or a biologist. From what I can gather from what was written, the article spotlights the publication of the first paper based on molecular dynamic simulations run on IBM's supercomputer Blue Gene/L run at the Computational Biology Center at the IBM T.J. Watson Research Center. The paper, published in http://www.bio-itworld.com/news/041805_report8136.html, described molecular interaction of a protein rhodopsin embedded in a bi-layer system containing cholesterol and two different lipids (I think we would call this as a membrane). From my meager understanding, this is a simulation of a specific protein in a complex environment. The Human Proteome Project that we are participating in here at the World Community Grid is studying the likely foldings of the many proteins found in the human system without the involvement of other complexities of the environment within which the protein exists. I would expect that the results of The Human Proteome Project might lead to other simulations such as this one.

I am going to ask the staff of the World Community Grid to move this thread into the Human Proteome Folding forum which is monitored by some of the research scientists at the Institute For Systems Biology. Perhaps one of them might care to comment on this.

hi carroll (?),

thank you for that info!
i understand just very little of thas proteome things...
i only wanted to know what WCG is related to that bluegene computings is, *if* it is.



thank you.
i guess it would be interesting to other users, too.

tom

Just my 2 cents more on this subject. The Blue Gene computer is really a general purpose supercomputer. It was used to study the mechanics of protein folding and other protein processes in great detail. You can think of it as simulating the individual atoms and electrical and chemical interactions among them to try to duplicate what really happens in nature.

The Human Proteome Folding project on World Community Grid uses the Rosetta program. This program was developed over many years to encode higher level rules about how proteins tend to fold and has been verified to fairly reliably predict the correct folds. Using Rosetta, scientists can figure out generally what shape a protein folds into rather quickly, versus the more detailed and time consuming simulations mentioned above. Thus, for the first time, it is now feasible, using grid computing, to do this for all of the genes.