Hey, what about some healthy competition ? ;-)

A while ago I tried to convince betterhumans members to join in and help with the protein folding efforts at Rosetta@home, sadly with very limited success. Since we now have a Folding@home recruitment thread, I just had to pitch in and try again:

I used to participate in Folding@home for a number of years (right from the beginning) but switched to Rosetta@home when they went public last September. I firmly believe that Rosetta@home is the better choice for those interested in the things (life extension and fighting the major killer diseases, nano tech, general technological advancement) that betterhumans members tend to be interested in. Also Rosetta@home is simply more fun: they are still a much smaller, growing project with very direct access to the scientists (ask them a question on their forum and they will respond).

Some links: Wikipedia article on Rosetta@home, my previous Rosetta@home forum post, a betterhumans news article on Rosetta@home disease related research, and a detailed comparison of various distributed computing (@home) science projects.

Rosetta@home and Folding@home - the basics:

Rosetta@home predicts the 3D structure of proteins from their amino acid sequence, so biomed scientists can deduce each protein's function in the cell processes. Rosetta@home also has the capability to design new proteins that perform specific functions in the body thereby opening up a new avenues to fight some of the mayor killer diseases (Alzheimer's, cancer, HIV...). The main emphasis of the Rosetta@home project is to improve the Rosetta software package which is available free of charge for academic use. The Rosetta software also is used by the Human Proteome Folding project (run on the world community grid, another distributed computing effort, sponsored and operated by IBM).

Folding@Home is an advanced Computational Chemistry project which studies how proteins fold. It's interested in the chemistry of unfolded, partially folded, and completely folded ("native") proteins, as they relate to one another. It does not attempt to predict protein structure from sequence, but tries to simulate the process of folding ... using Molecular Dynamics (the laws of physics) to show scientists  what actually happens during folding. ... This approach requires enormous amounts of computing power to simulate even small, fast-folding proteins, so currently it's not usable for protein 3D structure prediction (quoted from the above comparison of the distributed computing science projects).

I created a betterhumans team at Rosetta@home (currently with only myself as a member). Please come over to Rosetta@home, sign up and join our team.

Update (04-20-06): the team now has four members (Hi Joel). So, who wants to be number five ?? ;-)
Update (05-02-06): also see the new Rosetta@home team tread
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Hoelder1in

Now we are two.

 

I will try to see if I can join your team. I'm already a member.

When I view my preferencies, I show up as a member of betterhumans.com, but when I go to the team page, I don't show up.

Do I need to delete my current account or what?

So it sounds like Rosetta is restricted to specific cases of the general protein folding problem to answer more specific questions. While Folding is aimed at the more general question of how all proteins fold in general.

Seems like Rosetta may find answers faster than Folding and with more benefit to medicine.

I did a few units of Folding before switching back to SETI and the Mersenne prime search. I guess if I start this again, I should focus on Rosetta, right?

KOSMOS and chimaster, welcome to our new, fledgeling Rosetta@home team, great to have you onboard ! So lets hope we mange to attract a few more fellow betterhumans to make this more fun. Also, since my computer is turned off over the Easter weekend, I wont be able to contribute credits to the team before I am back home on Tuesday.

@chimaster: the team page should list your name once you have contributed credits to the team (after your next WU upload).    

@ Mr. Farlops: it would be be great if we could also welcome you as a member of the new team !

I guess in a nutshell one can say that while Folding@home is interested in understanding how proteins fold, Rosetta@home tries to determine the end points of the folding process, i.e., the 3D shapes of the folded proteins. Since the latter task is much less computationally demanding (requires less computer time) there is a good chance that eventually it will be possible to use the Rosetta software to compute the 3D shapes of tens of thousands of proteins for which their 3D shapes are not yet known. Currently, determining the 3D shapes of proteins requires time consuming and expensive experiments. So this would be a big advantage. In contrast, Folding@home is not predominately interested in the folded states the proteins, but rather in the intermediate, partly folded (or in some cases mis-folded) states. Calculating all those intermediate states takes a lot of computing time. So the Folding@home algorithm isn't really designed to determine the shapes of large numbers of  proteins. Note, that once the shape of a protein is known, the function the protein performs in the body can be determined from its shape  - which is where the medical relevance comes in ! And most importantly of all, the Rosetta algorithm also allows to design new proteins to order, that don't exist in nature, to perform specific functions in the body. This is where it starts getting really cool: one can think of these 'designer proteins' as Drexlerian nanobots that go into the cells to perform specific functions there, such as blocking disease causing processes, breaking up unwanted chemicals, or even fixing errors in the genome. And all of these things will happen sooner if lots of participants donate their spare computer time to Rosetta ! 
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Hoelder1in    

Thanks for spearheading this initiative. Let me know if there's anything I can do to help promote the team.

- S

Simon:

Thanks for spearheading this initiative. Let me know if there's anything I can do to help promote the team.

I am glad you liked the idea to have a betterhumans team at Rosetta@home and thanks for offering to help with promoting the team. :-) Is there anything specific you had in mind ? Anything would be welcome from my point of view. One thing I was thinking about was a dedicated Rosetta team thread in the science forum  which perhaps could be kept alive with occasional updates about the project or better  still by  science/technical discussions of the team  members  (assuming that  some critical mass is reached). One could of course also think of a link to Rosetta from the homepage (there is lots of unused space below the tee-shirt ad ;-) - anyway, just an idea.

-H.
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Hoelder1in

I like the suggestions. Sorry for the delay. What with hackers and all, some busy times. I'll try to find a way to highlight the project somewhere on the site. Highlighting it somewhere in the left-hand ad box is a good idea, but it may make the box run too long for short pages. I'll see what I can do.