From David Kim last year:

Do you have any suggestion to PP@H users like me about how to decide which project to join, since they have some researching contents in common?

Q1. Insist on PP@H or turn to R@H?
Q2. R@H is a non-profit or profit project? I can't find any related explanation on your site.




It is up to the volunteer to do research and decide. Optimally, you can help both projects...or all projects for that matter! Both projects are doing research for similar goals but using different methods. Helping both projects would benefit science..not one or the other.

Q1 - both!
Q2 - R@H is non-profit and for science, all results will be available to the public. The Rosetta application is licensed to pharma but most of the proceeds go to further research, for example - it funds an annual Rosetta development conference that brings researchers from various universities together. The application is available for free to academic users.

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And from David Baker:

Hello,

I have a few quetsions that do not seem to be answered on the wesite:

1) Who will own the results of rosetta@home? Will it be public domain? Will a (private) research institute own it?

2) Will the rosetta@home results lead to the patenting of genes, proteines, etcetera?

3) What's the difference/relation of rosetta@home with folding@home and predictor@home? Aren't you just duplicating research here?

Thanks to anyone who can answer these quetions for me. Oh, and you might want to put these in a FAQ on the site. I don't think I'm the only one who likes to know!



1) Everything will be public domain
2) No, I do not believe in patenting naturally ocurring genes, proteins, etc.
3) Rosetta@home is very different from folding@home. rosetta@home aims to predict naturally
ocurring protein structures and design new and useful ones; folding@home is simulating the process of protein folding. predictor@home is also working on structure prediction, but with a very different method.

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Interesting thread. I realize that the research is going to be provided freely to the public and then private companies can use it to make drugs to sell for profit. If that happens, then so what? They make a drug, profit from it after its release for the length of the patent, then a generic version can be produced and we are all better off as a result. Also, as a whole science and medicine would be greatly elevated if biology (and proteins) could become a predictive science.

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Admin/TestPilot:
(Since your name is causing a little confusion, would you mind creating a 3rd account named TestPilot2 and using that?)
We've had discussions with David Baker about how this project will deal with potential treatments (the results), how the software is licensed (free for academic use, although commercial use has to pay fees), and what those fees are being used for.

"The Results" were said to be free to academia, if not commercial interests, too. That's the way Keith Davies (THINK) at FaD dealt with FaD's collection of results.

Not-For-Profit organizations in the USA doesn't mean that they don't charge anything for their services/products. A local day care center was a NFP organization that charged the parents for watching the kids during the day. The fees collected were used to pay utilities, expenses like food toys, maintenance, and wages of the employees.

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Rosetta at home is freely available (including the source code) to academic users. Companies are required to pay a fee to use it because they will be profiting from it so it is only fair. Besides, most companies probably need to pay a fee so that if they do develop a marketable product using the software, they will not have any problems with their lawyers telling them they should have bought the rights first.
The main reason that the source code is not easily available to everyone else is because people on these message boards expressed concerns that there is a small but significant fraction of people who would exploit the source code to increase their BOINC credits or do other mischief. It seems reasonable that the risk of harm to the Rosetta@Home community should be minimized.

As far as cures for various diseases goes, any company that licences Rosetta and develops a drug using Rosetta will be free to patent the drug (but will have no rights over Rosetta itself) and make whatever profit it sees fit. As for therapeutics that we in Bakerlab and collaborating labs are working on, nobody here is doing this to get rich. We are doing this because we believe we can make a contribution to the world, and help people who desperately need help. Case in point: AIDS drugs (eg "protease cocktails") that are the current best treatment for HIV/AIDS cost thousands of dollars per month of use, and are out of reach for most third world patients. We are trying to develop a vaccine which would be cheap and effective, and would directly help those who suffer most from the scourge of HIV.

I hope that clarifies things a little.

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The purpose of the project is to improve methods behind the Rosetta software.
Rosetta is closed source package with very restrictive license. So Any findings Rosetta@Home makes are made freely available to everyone is a lie.

I think you may be mixing up the Rosetta algorithm i.e. the actual code that performs the calculations, with the result of running that code, which is the protein structures.

The code is closed source, subject to licensing costs. This places a limit on who can run it.

The RESULTS are not closed source (at least not those that we are working on), those can and will be published.

As an example, if David Baker and the team over at Bakerlab come up with a protein structure that can be used as an HIV vaccine, they'll publish it. Trust me, they will.

In that situation, it's a case of "We're not going to tell you exactly how we produced this protein (close source algorithm), but here it is. Go out and make it to cure HIV (published results)."

Do you see the difference now?

The method is closed, the results are not. Kinda like Col. Sanders "secret recipe of 11 herbs and spices" at KFC. They won't tell you what those herbs and spices are, but they sure publish (sell) a lot of the results, tons and tons of KFC a year.

-- Edit -- Damnation - Vanita beat me to the punch. :)

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Nobody is twisting anyones arm to crunch for R@H. If you have significant misgivings about this type of research, then by all means go to another project.

The whole DC movement of which I have been apart of since the late 90's has always been based on Voluntary Grass Roots efforts to try and solve problems not readily approchable by standard methods.

This is actually one of the better and more pragmatic of the projects I have been apart of. Because it needs such a huge amount of proccesing power to attack the Protien Folding Problem most participants hate to see even one computer leave.

David Baker has stated on many occasions from the projects beginings that the Protien Folding Problem is solvable if only the correct amount of proccessing power can be applied to it. THIS IS WHAT THIS PROJECT IS DOING. Once this is done the methods have far reaching implications for many displines beyond Bio Chemistry.

See Ya..............

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It's always tough to see someone go. If their heart is truly not in it (and maybe sometimes their mind gets in the way), then we should simply bid them farewell and thank them for their contribution.

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I know people will not like what I'm going to say, but I say it anyway.

AIDS/HIV gets much attention nowaday. Big (expensive) conferences, big names talking, heads of different foundations promising this and that. I don't think it's because it's a big problem especially in Africa, it's because it's a problem here in "western world". In this very thread there is a link to an article about possible Malaria vaccine. What was more interesting to me in that article was the sentence: "Malaria is the leading killer of children under five in sub-Saharan Africa". Malaria gets very little attention and we know why. It's not a problem here, it's a problem somewhere there. Why bother, they are dying anyway to all kind of diseases. It's of cource totally unfair to put these two terrible problems against each other, but life is not fair. Life is just a series of choices, you cannot do everything.

I (and my box) are still very new in this crunching business and my contribution anyway is (and will be) insignificant, compared to the Power Crunchers and big teams that get all the attention. It's more like a naive hope that maybe it could still make a difference. It's like a drop in a rain. Somewhere people are desperately waiting for a rain. But what if the rain doesn't go there, but somewhere where it's not even needed. R@H is creating raw material. Big pharmas can use that material. They might find a cure for AIDS, good. They might find a vaccine for Malaria, even better. But only if they can make money with it. My ultimate night-mare is that my little contribution goes to something totally useless, like Fat Pill. That would be the ultimate money machine for that big pharma. Another "lifestyle drug". Feeling depressed, take a pill. Feeling too happy, take a pill. Gaining weight, take a pill. When you go to McDonalds you just order "Big Mac, large Diet Coke and medium Diet Pill. To go, thank you". Again you don't need to take responsibility for your actions.

I know I'm too pessimistic, R@H results will be used also for good. But it would be nice to have some guarantees that what ever you are crunching, is meaningful. In the beginning I was refering to Malaria and that's something I would like to do. A@H seems to do that (in a way), but they are not taking anyone in at the moment. Hopefully at some point...

Anyway, I will keep on crunching for R@H...for the moment.

Don't be too pessimistic. Who would have thought 15 years ago that the "Human Genome Project" would have an entire human DNA string mapped out? In fact the knowledge gained from that would open so many doors including a huge influence on what this project is doing.

Granted, what we're doing is helping improve programming methods used in prediction. However if you noticed the (LARS) units that we recently ran seemed to exclude much of the randomness and did a much better job at clustering toward the lowest energy and (RMSD). If this trend continues then we should see a gradual reduction in the "randomness" of serches.

As to what desease gets the attention? A large part has to do with the news media. They set the public health agenda and all of the big contributors seem to follow. Just keep in mind that if success in AIDS happens as a result of protein research, then other protein related deseases will be within reach.

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MFManager makes some good points re. malaria. We support the Malaria Control project as well as R@H. Both projects are very worthy in their respective fields and deserve attention...Cheers, Rog.

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My ultimate night-mare is that my little contribution goes to something totally useless.

Rosetta is working on Malaria as well as AIDS and cancer... and their technology will some day be used to address viral outbreaks such as bird flu when they occur.

Even if big pharma somehow manipulates things to their favor in the short term, in the long term there will be cures available for diseases and conditions that doctors presently consider untreatable. So, when compared to having no cure possible, that's pretty good, regardless of price.

Also, the methods developed with Rosetta will eliminate much of the trial-and-error approaches to drug development as it is done today. And this will eliminate much of the cost and many of the failures that presently occur in drug development.

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Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/