DISCUSSION of Rosetta@home Journal (5)

Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (5)

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David Baker
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Message 73000 - Posted: 6 May 2012, 0:43:35 UTC

We are VERY excited about the big jump in compute power-this will make a BIG difference. Thanks to all of you!!
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Message 73002 - Posted: 6 May 2012, 3:12:12 UTC - in response to Message 72916.  

BOINC Synergy based in Australia but with members all over just voted to make Rosetta Project of the Month for May 2012! Hope that helps with CASP 10!

The Knights Who Say Ni! are joining you with Rosetta as PotM for May!

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Message 73811 - Posted: 11 Sep 2012, 9:42:45 UTC

From the article link in home page:

\"Baker said the most promising discoveries are licensed to private companies to carry on the research and find out if the proteins really do what researchers thought they would do. \"We do simple things, then license the results to a pharmaceutical company,\" he said.\"

I always thought that the results were public, open.....
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David Baker
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Message 73846 - Posted: 16 Sep 2012, 18:16:05 UTC

All results of rosetta@home are public. as has been discussed before in these forums, the only way to actually get a potential drug into the clinic is to have a company license potential drug candidates from the university and spend the $$$ required for testing. if the company does not pursue this actively, they lose the opportunity and the university finds another company to develop the drug.

as I pointed out before, this is illustrated by the fact that the Gates foundation (and other charities) will not fund projects if there is not a clear plan for companies to develop possible drug candidates that come out of it, because they know that without this the things that are discovered will never contribute to improving health.
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Message 73850 - Posted: 16 Sep 2012, 23:56:04 UTC

Would it be correct to say that as your lab discovers protein structure prediction techniques, these techniques are published and publicly available... but as the technique is used to develop a specific protein drug therapy that the drug candidate is licensed, i.e. owned by some non-public entity?

So example, there are now work units studying Ebola virus. We will be donating our computing time to help you study the Ebola virus. You might code up some new techniques in an effort to reach an accurate structure prediction sooner, or reach an accurate prediction for a structure with unique properties that make it less predictable using the prior techniques. And then the outcome of our crunching would be... what? A short-list of drug candidates? Or target sites? Or structure prediction techniques? At what point, and which of those, would things go private and under license?
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Message 73852 - Posted: 17 Sep 2012, 7:04:51 UTC

The ebola work units are designing small proteins to bind to the Ebola virus. we will collect the results from all of the runs, and test those predicted to bind the virus most tightly in our experimental lab. the proteins that do bind the virus will then be tested to see if they block the virus from infecting cells. if they do, the next step is to see if they can be used as drugs to block Ebola infection. this we cannot do in my lab. a government agency could take this over for testing in a specialized lab, or the university could license to a company on the condition that the company push forward on getting the designs into the clinic
as fast as possible.
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Message 73857 - Posted: 18 Sep 2012, 19:05:48 UTC - in response to Message 73852.  

a government agency could take this over for testing in a specialized lab, or the university could license to a company on the condition that the company push forward on getting the designs into the clinic as fast as possible.


Thanks for the answer!!!

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Message 74069 - Posted: 22 Oct 2012, 1:38:05 UTC

I have exciting news. We and the University of Washington are starting up a new Institute for Protein Design to design new proteins to address current challenges in medicine, energy, and other areas. You can learn more about the institute at http://depts.washington.edu/ipd/. Rosetta@home is and will continue to be a critical part of our efforts. For every new potential protein therapeutic we design, we use Rosetta@home to test whether it will actually fold into the desired structure. And we need help! We have quite a backlog of exciting new designed proteins to test on Rosetta@home because we are designing proteins for quite a range of problems-new anti flu proteins, anti-cancer proteins, and new materials--and it takes 3000-5000 work units to test each one. This Rosetta@home testing is becoming the slow step in the whole design process, often taking over 10 days to complete. So please tell your friends and relations to join us!

A generous donor has provide funds which we want to use to invite 5-10 Rosetta@home participants to visit the Institute and see what we are trying to accomplish first hand. More on this in my next post.


Exciting news indeed. I\'m wondering what ways would attract and retain new users.
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Message 74070 - Posted: 22 Oct 2012, 2:02:03 UTC - in response to Message 74069.  
Last modified: 22 Oct 2012, 2:02:27 UTC

I have exciting news. We and the University of Washington are starting up a new Institute for Protein Design to design new proteins to address current challenges in medicine, energy, and other areas. You can learn more about the institute at http://depts.washington.edu/ipd/. Rosetta@home is and will continue to be a critical part of our efforts. For every new potential protein therapeutic we design, we use Rosetta@home to test whether it will actually fold into the desired structure. And we need help! We have quite a backlog of exciting new designed proteins to test on Rosetta@home because we are designing proteins for quite a range of problems-new anti flu proteins, anti-cancer proteins, and new materials--and it takes 3000-5000 work units to test each one. This Rosetta@home testing is becoming the slow step in the whole design process, often taking over 10 days to complete. So please tell your friends and relations to join us!

A generous donor has provide funds which we want to use to invite 5-10 Rosetta@home participants to visit the Institute and see what we are trying to accomplish first hand. More on this in my next post.


Exciting news indeed. I\'m wondering what ways would attract and retain new users.


more stories from rosetta@home about diseases that effect them or someone they know.. like cancer Parkinson\'s diabetes ect..
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Message 74153 - Posted: 1 Nov 2012, 15:31:31 UTC

The new Institute sounds amazing. If I can give you one tip, post updates about your research as much as possible to keep people motivated to use Rosetta and Foldit.
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Message 74214 - Posted: 8 Nov 2012, 22:25:24 UTC

With your help, we have made an exciting breakthrough in protein design that is reported in a research article titled \"Principles for designing ideal protein structures\" in the journal Nature today. You can read about it at

http://www.nature.com/news/proteins-made-to-order-1.11767

In this paper, we describe general principles for creating new proteins from scratch. The new Institute for Protein Design is using these principles to design new proteins to treat disease.

Rosetta@home was absolutely critical to this work as described in the news article; Figure 3 in the paper shows how all of your contributions were used to test designed sequences to see if they folded up to the right structure. Most of the work units we are sending out on Rosetta@home these days are for exactly these kind of tests on the new proteins we are designing--this is absolutely critical to the research and to the development of new therapeutic and other functions. Thank you again for all of your contributions!


I\'m happy to hear that Roseeta@Home is making progress. It\'s an honor to crunch for you ;)
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Message 74225 - Posted: 9 Nov 2012, 16:36:27 UTC - in response to Message 74214.  

With your help, we have made an exciting breakthrough in protein design that is reported in a research article titled \"Principles for designing ideal protein structures\" in the journal Nature today. You can read about it at

http://www.nature.com/news/proteins-made-to-order-1.11767

In this paper, we describe general principles for creating new proteins from scratch. The new Institute for Protein Design is using these principles to design new proteins to treat disease.

Rosetta@home was absolutely critical to this work as described in the news article; Figure 3 in the paper shows how all of your contributions were used to test designed sequences to see if they folded up to the right structure. Most of the work units we are sending out on Rosetta@home these days are for exactly these kind of tests on the new proteins we are designing--this is absolutely critical to the research and to the development of new therapeutic and other functions. Thank you again for all of your contributions!


I\'m happy to hear that Roseeta@Home is making progress. It\'s an honor to crunch for you ;)




This is great. Amazing!!!

Tom Zolotor

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Message 74240 - Posted: 10 Nov 2012, 15:17:13 UTC - in response to Message 73852.  

I have exciting news. We and the University of Washington are starting up a new Institute for Protein Design to design new proteins to address current challenges in medicine, energy, and other areas. You can learn more about the institute at http://depts.washington.edu/ipd/. Rosetta@home is and will continue to be a critical part of our efforts. For every new potential protein therapeutic we design, we use Rosetta@home to test whether it will actually fold into the desired structure. And we need help! We have quite a backlog of exciting new designed proteins to test on Rosetta@home because we are designing proteins for quite a range of problems-new anti flu proteins, anti-cancer proteins, and new materials--and it takes 3000-5000 work units to test each one. This Rosetta@home testing is becoming the slow step in the whole design process, often taking over 10 days to complete. So please tell your friends and relations to join us!

A generous donor has provide funds which we want to use to invite 5-10 Rosetta@home participants to visit the Institute and see what we are trying to accomplish first hand. More on this in my next post.


Hi, David! I joined yesterday and just in time for this exciting new development! Looking forward to participating and making a positive difference.

By the way, how can proteins be used for energy and for new materials? The possibilities seems endless.
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Message 74254 - Posted: 11 Nov 2012, 19:58:41 UTC

One way they can be used for energy that I believe I\'ve seen Dr. Baker refer to before is that the proteins can be a catalyst. Much like the yeast makes corn into ethanol that can be used to power your car. If I recall he made reference to the potential for a protein that could break down tougher plant fibers and basically extract much of the energy that you release when the plant burns.

For new materials, I believe it is possible (feasible anyway) to string together proteins into stands like spider\'s silk. From that you could make fabrics with interesting properties, such as repel water, insulate the body, bullet proof, whatever. What if the fibers expand when they get cold, and contract when they get warm? Then you\'d have a coat that allows more air flow through it on warmer days.

He has also talked about sequestering carbon dioxide from the atmosphere using proteins to make the process happen much faster than the algae in the oceans.
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Message 77627 - Posted: 5 Nov 2014, 3:25:38 UTC

In folding, can a protein end up in an intermediate state, but not in its
lowest energy state? Or, do all proteins manage to arrive at the lowest
state?

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Message 79277 - Posted: 22 Dec 2015, 13:18:38 UTC

Is David Baker\'s Rosetta@home Journal continued at all? The last post is more than a year old.

Michael.
Michael H.W. Weber
Chairman and scientific advisor of Rechenkraft.net e.V.

http://www.rechenkraft.net - The world's first and largest distributed computing association. We make those things possible that supercomputers don't.
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Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (5)



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