Hello thom217,

I can offer my opinion to answer your question #1. We cannot even fold every protein directly expressed in the human genome since some are just too long for the algorithm used by Rosetta to fold reliably. We are restricting ourselves to the shorter proteins. So there are many proteins that this project will never try to fold. But we are not restricting ourselves to the human genome. We are also looking at a number of other species, such as malaria, which are also important for people and for which some genomic data is available.

The Human Proteome Folding project is not going to provide a final definitive list of proteins. It is just what we can do in this first decade of the 21st century.

mycrofth

Rich made a long post back in May listing some of the pathogens (no cute cuddly pets) and other microbes here: http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=2885

This is not the complete list. He got tired of typing. I expect we will see it all when they start publishing papers.

vep........that "stranger" tag merely reflects your post count.

I think they could do with getting more friendly tags

Re: [By the way, I don't know why I'm called a stranger: I'm crunching since 20 november 2004.]

The forum software (mvnforum) gives this tag to members who have not yet posted many times in the forum. As you post more often, your tag will change.

Hello JJ,

If you read the 12 Aug 2005 status update at http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=3563#26720 then you will notice:

What this means is that we are part of a chain. Baker Lab at the University of Washington has developed and tested the Rosetta program and made it available to the scientists of the world by various means, such as the online Robetta server which accepts individual molecules and uses a version of Rosetta to fold them. The ISB web page about the HPF Project links to the Baker Lab at UW, which maintains all the papers they have done online for your perusal, though you will have to search elsewhere for other papers referencing Robetta and Rosetta as a research tool. Now the ISB is running Rosetta over a large number of proteins (using the World Community Grid and our computers) and soon will make them available online, starting with a yeast database.

We are very interested in the papers that shall be published in years to come citing these databases as sources. I expect that we shall maintain a list of them somewhere, but that is all 'pricing the unborn calf'. For now, the experiment (or project, depending on terminology) is still running.

mycrofth