Pharyngula

Posted by: Andrew | January 17, 2007 3:04 PM

"Almost all human diseases are caused by mutations in proteins that effect their 3-d structures..." Is this true?

Posted by: Sarcastro | January 17, 2007 3:24 PM

So is rosetta@home kind of a new kid on the block competing with folding@home, which has been running since 2000?
Or are they complimentary?

Complimentary.

I know Baker and Ranganathan and their work very well and (like the rest of the protein community) find their work very important and impressive. However, Rosetta@home and Folding@Home are addressing very different problems. Rosetta only predicts the final folded state, not how do proteins fold (and Rosetta has nothing to do with protein misfolding). Thus, those methods are not useful for the questions we're interested in and the diseases we're tackling (Alzheimer's Disease and other aggregation related diseases).

Also, one should note that accurate computational protein structure prediction is still very challenging compared to what one can do experimentally, whereas the information obtained from Folding@home on the nature of folding and misfolding pathways matches experiment (e.g. with quantitative validation in rates, free energy, etc) and then goes beyond what experiment can tell us in that arena. While Rosetta has gone a long way and is a very impressive project, given the choice between a Rosetta predicted structure and a crystal structure, one would always chose the crystal structure. I bet that will be changing due to their great efforts, but that may still be a ways off for that dream to be realized.

So, both are valuable projects IMHO, but addressing very different questions. I think there are some misunderstandings out there, though. Some people think FAH is all about structure prediction (which it is not -- that's Rosetta's strength) and some think Rosetta is about misfolding related disease (which it's not, that's Folding@Home's strength). Hopefully this post helps straighten some of that out.

Posted by: Graham Douglas | January 17, 2007 3:30 PM

Erm... do you mean "complementary"?

Sorry.

Posted by: craig | January 17, 2007 4:21 PM

"Erm... do you mean "complementary"?"

that too.

Posted by: HP | January 17, 2007 4:54 PM

j: Really. He's the principle investigator for one of two complimentary programs. It's listed right there on the calender, next to the box of stationary.

Posted by: Kseniya | January 17, 2007 6:13 PM

Check out grid.org, too.

Posted by: Anna | January 17, 2007 8:18 PM

And there is also there climateprediction.net, which started in 2003 and runs on the same platform as SETI (BOINC). Seems like there could be a fair amount of competition between projects as people are unlikely to sign up for more than one, especially because the software is incompatible.

Posted by: Kseniya | January 17, 2007 9:35 PM

The software may be incompatible, one with the other, but can very likely coexist. I have a GRID agent running, and all it does is download a problem, solve it, upload the results, and grab a new one. There's no reason why multiple agents (of different types) can run on the same PC and do more or less the same thing.

Having more than one agent running at idle priority on your PC only means that they'll share those spare "unused" cycles, and take longer to complete. One agent would eclipse the other only if it were to run at a higher priority - which is unlikely, because the whole "unused cycles" concept relies on the agent running at idle priority.

I agree that it's a great idea. The virtual super-computer. The GRID site has a stats page, where you can see how many, many thousands of CPU-years are contributed annually by users like us. That's a lot of computing power, but is only a small fraction of what it could be.

Posted by: BlueIndependent | January 17, 2007 11:11 PM

SETI I believe was in fact the first to do this. It makes a lot of sense for any sceintific endeavor in general actually, from the human genome project, to just about anything.

But this begs the question from me: is there a standardized database or library that is freely accessible over the internet that is an authoritative compilation of the study of evolution? Such a thing as this made available through everyone's internet browser could certainly help efforts to spread the word and the knowledge. Think about it: kids these days tend to outshine their parents when using PCs, so it would be a smart way of tapping into their newfound capabilities, while enhancing their research skills for school, and showing the benefits of science.

Posted by: Ritchie Annand | January 18, 2007 12:11 AM

I split my BOINC time between SETI@Home, Predictor@Home and rosetta@home, though Predictor@Home has nothing going on at the moment:

NOTE: Predictor@Home is offline while we implement new methods of protein structure prediction. The Mfold series of work has concluded. You can find information about other projects you may want to contribute to here: http://boinc.berkeley.edu/projects.php

Folding@Home/Genome@Home were fun to run. I was hoping they would tag along in the BOINC framework as well, but it was not to be. The proteins were filled with alpha helixes and beta hairpins - I'd love to know how prevalent these are in all proteins.

The combination of the purely speculative yet amazing it if happens (SETI; happier now that they have an optical program too) with some good biological science computing (rosetta, etc.) just appeals.

Stats so far: 36533 on SETI (not sure if this includes my earlier non-BOINC stuff), 23569 on Predictor, and 2886 on Rosetta.

I gotta ask, though. Why isn't there a Rosetta@Home team for scienceblogs or pharyngula??

Posted by: laurelin | January 18, 2007 10:25 AM

"Listen carefully: she says "within the nuc-you-lus.""

yeah, well, you try focusing on enunciating all those damn words and see if you make a mistake :)

I'm surprised that more people haven't complained about the voiceover. I was a little nervous about leaving myself in there but a bunch of people recommended that I do so. It was supposed to be just a placeholder.