DISCUSSION of Rosetta@home Journal (4)

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David Baker
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Message 58510 - Posted: 5 Jan 2009, 6:02:42 UTC - in response to Message 58468.  

If I\'m reading the results correctly (its not the easiest table to interpret and there\'s a ton of information in there), it seems that R@h did better overall in CASP8 than any of the other 164 participants. That\'s wonderful!

That\'s also what I make of it. And if I\'m right, we don\'t just win in a close call, we win hands down!
If this true, it should in my opinion be front page news! This is fantastic!


Although I wasn\'t able to attend, my understanding is that this was also the consensus at the CASP8 assessment meeting held last month in Sardenia. Thanks everybody for their contributions!

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Message 59050 - Posted: 27 Jan 2009, 4:04:57 UTC

I and maybe others might need a refresher in what is a native structure. Thanks
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Message 59054 - Posted: 27 Jan 2009, 7:30:12 UTC - in response to Message 59050.  

I and maybe others might need a refresher in what is a native structure. Thanks


Sorry! For a subset of proteins, the structure has been determined using very time consuming and expensive experimental methods such as x-ray crystallography and nuclear magnetic resonance. the three dimensional structures obtained in these experiments are thought to closely resemble the structures the proteins adopt when they function in our bodies or elsewhere, and these are referred to as \"native\" structures.

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Nickhorsky

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Message 59082 - Posted: 28 Jan 2009, 3:53:53 UTC

Thanks for the lesson. I\'m not sure where this will all lead but the future is ours. One can only dream of the doors that may open. I was great at Chem but my biology grades sent me to a different career path.
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Max DesGeorges

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Message 59178 - Posted: 30 Jan 2009, 3:23:40 UTC - in response to Message 58468.  


That\'s also what I make of it. And if I\'m right, we don\'t just win in a close call, we win hands down!
If this true, it should in my opinion be front page news! This is fantastic!

I\'m agree.
CASP8 results in the front page would be a good idea. It would give a positive feedback to all participants.
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Message 60048 - Posted: 9 Mar 2009, 19:07:36 UTC

Thanks for all the details on the papers and work in progress in BakerLab.

Will these papers be referenced on the homepage when they are released?
If you can continue to give WU names as they relate to the various papers, that helps people understand what they\'re working on right now (or did in the past).
If having a DC project with BOINC is of interest to you, with volunteer or cloud computing resources, but have no time for the BOINC learning curve,
use a hosting service that understands BOINC projects: http://DeepSci.com
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David Baker
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Message 60052 - Posted: 10 Mar 2009, 3:51:01 UTC - in response to Message 60048.  

Thanks for all the details on the papers and work in progress in BakerLab.

Will these papers be referenced on the homepage when they are released?

Yes, we will try to do this. There is also a relatively complete list on my group web page.

If you can continue to give WU names as they relate to the various papers, that helps people understand what they\'re working on right now (or did in the past).


Yes--we will keep doing this as much as possible!

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Message 60056 - Posted: 10 Mar 2009, 10:15:16 UTC

Thanks for these excellent and hugely motivating updates. For some of us, updates like those 5 make a real difference - please keep similar information coming as and when possible.

You should really publicise your successes more, even if just on the front page of this site. For instance, despite being a fairly committed and long-standing cruncher, I had no idea that you/we were the best-ranked group at CASP8. I\'d have that in a big banner on the front page if this was my website!

Keep up the great work.
Alver Valley Software Ltd - Contributing ALL our spare computing power to BOINC, 24x365.
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Message 60088 - Posted: 12 Mar 2009, 4:42:48 UTC

On manuscripts 2, 5 & 6 I believe I understood enough to be able to say \"wow\"!
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Message 60102 - Posted: 12 Mar 2009, 16:30:18 UTC

Ya, wow! The only reason there isn\'t more discussion on these items is that we\'re all still trying to put our chins up closer to the roof of our mouths again. Thank you for sharing more about the activities from inside BakerLab.

...any news on the CO2 sequestering enzyme ideas? or the HIV drug candidates that were submitted last year?

I\'m curious about the uniqueness of 20 AAs in my DNA as compared to other people. I realize that something less then 1% of my DNA differs from the next humans, but with billions of genes, it would seem as though the DNA slicer stands a chance of \"repairing\" a gene that\'s working fine in *MY* body, perhaps on some other DNA strand.

I suppose if you consider that you only inject such a thing into the body of a person with the target disease, it dramatically reduces the potential for adverse side-effects. And I suppose as well that it\'s possible the beneficial effects could easily exceed the detrimental effects. But, I was wondering about this 20 AA fragment. How likely is it that all the patients have the same AAs around the problem area? And how likely is it that some other area of a given person\'s body happens to have the same strand portion serving some other useful purpose?
If having a DC project with BOINC is of interest to you, with volunteer or cloud computing resources, but have no time for the BOINC learning curve,
use a hosting service that understands BOINC projects: http://DeepSci.com
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Message 60106 - Posted: 12 Mar 2009, 21:47:10 UTC

I have a question regarding manuscript 3 from earlier this month. Mr. Baker describes RosettaLigand as very succesful in predicting pharmacologic interactions, but results are not public due to requirements of pharmaceutical companies using these predictions. I am questioning the information on home page of this project - Rosetta@home is not for profit. That was main reason I quit Predictor@home and started Rosetta. Is therefore possible that my computers were working on some results for private company that does not want to disclose the results now? I do not wish any of my machine work for private company. I pay for electricity and hardware, therefore any work for private companies should be optional with option not to participate.

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Evan

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Message 60107 - Posted: 12 Mar 2009, 21:55:52 UTC - in response to Message 60106.  

I have a question regarding manuscript 3 from earlier this month. Mr. Baker describes RosettaLigand as very succesful in predicting pharmacologic interactions, but results are not public due to requirements of pharmaceutical companies using these predictions. I am questioning the information on home page of this project - Rosetta@home is not for profit. That was main reason I quit Predictor@home and started Rosetta. Is therefore possible that my computers were working on some results for private company that does not want to disclose the results now? I do not wish any of my machine work for private company. I pay for electricity and hardware, therefore any work for private companies should be optional with option not to participate.



I believe that it was said somewhere last year or so that the Baker Lab is not allowed to receive payments from private companies. Also the pharmaceutical companies would not want their products run on a public network as someone could possibly decipher some of their secrets. In addition it would also probably breach the strict rules that apply to patents.
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Message 60109 - Posted: 12 Mar 2009, 22:15:02 UTC - in response to Message 60107.  

I have a question regarding manuscript 3 from earlier this month. Mr. Baker describes RosettaLigand as very succesful in predicting pharmacologic interactions, but results are not public due to requirements of pharmaceutical companies using these predictions. I am questioning the information on home page of this project - Rosetta@home is not for profit. That was main reason I quit Predictor@home and started Rosetta. Is therefore possible that my computers were working on some results for private company that does not want to disclose the results now? I do not wish any of my machine work for private company. I pay for electricity and hardware, therefore any work for private companies should be optional with option not to participate.



I believe that it was said somewhere last year or so that the Baker Lab is not allowed to receive payments from private companies. Also the pharmaceutical companies would not want their products run on a public network as someone could possibly decipher some of their secrets. In addition it would also probably breach the strict rules that apply to patents.


If that is true how is possible that RosettaLigand is used by private companies? What is relationship between resources provided by Rosetta and private research?
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Message 60111 - Posted: 12 Mar 2009, 22:25:24 UTC

He said very clearly that \"RosettaLigand was successful\", not that Rosetta@home was used in the work done by the pharmeceutical company. He also distinguished between the \"private set of compounds\" provided by that company, and the \"public datasets\" that BakerLab had run the program against.

So, the company is using some of the tools, and provided feedback to BakerLab both on the usefulness of the program as it is today, and some areas where it may be further improved.

If such a drug company sent out work units to your machine to study a new drug or \"private compound\", they would be sending the amino acid sequence of that compound out to the world, essentially making it public domain! Trust me, drug companies don\'t operate that way.

So, BakerLab is working to improve the tool on a non-profit basis. And drug companies are working to use such tools to attack specific diseases/viruses etc. Read my prior comments on intellectual property rights here
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Message 60112 - Posted: 12 Mar 2009, 22:28:22 UTC - in response to Message 60110.  


If that is true how is possible that RosettaLigand is used by private companies? What is relationship between resources provided by Rosetta and private research?


Evan didn\'t say private companies couldn\'t use RosettaLigand. They said BakerLab is \"not allowed to receive payments from private companies\".
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Message 60115 - Posted: 12 Mar 2009, 22:36:41 UTC - in response to Message 60111.  

He said very clearly that \"RosettaLigand was successful\", not that Rosetta@home was used in the work done by the pharmeceutical company. He also distinguished between the \"private set of compounds\" provided by that company, and the \"public datasets\" that BakerLab had run the program against.

So, the company is using some of the tools, and provided feedback to BakerLab both on the usefulness of the program as it is today, and some areas where it may be further improved.

If such a drug company sent out work units to your machine to study a new drug or \"private compound\", they would be sending the amino acid sequence of that compound out to the world, essentially making it public domain! Trust me, drug companies don\'t operate that way.

So, BakerLab is working to improve the tool on a non-profit basis. And drug companies are working to use such tools to attack specific diseases/viruses etc. Read my prior comments on intellectual property rights here


Thanks for the link. If I understand it correctly RosettaLigand is available for anybody who wants to use it including pharmaceutical companies, but they have to use their own resources to run it and Rosetta does not do any computations for them?
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Message 60117 - Posted: 12 Mar 2009, 22:55:48 UTC
Last modified: 12 Mar 2009, 22:58:45 UTC

Perhaps this is the details you are looking for??

...avaialble at no charge to non-profit users and on an annual fee basis to commercial users


Note that I did not assert Evan\'s quote was accurate. The above seems to contradict what they said.

So, in other words, this company must have paid a fee to use the software, and yet was willing to take the time required to provide the feedback anyway. Because they want to see the science of the tool improve as well.
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Message 60119 - Posted: 12 Mar 2009, 23:21:46 UTC - in response to Message 60109.  
Last modified: 12 Mar 2009, 23:32:30 UTC

I have a question regarding manuscript 3 from earlier this month. Mr. Baker describes RosettaLigand as very succesful in predicting pharmacologic interactions, but results are not public due to requirements of pharmaceutical companies using these predictions. I am questioning the information on home page of this project - Rosetta@home is not for profit. That was main reason I quit Predictor@home and started Rosetta. Is therefore possible that my computers were working on some results for private company that does not want to disclose the results now? I do not wish any of my machine work for private company. I pay for electricity and hardware, therefore any work for private companies should be optional with option not to participate.



I believe that it was said somewhere last year or so that the Baker Lab is not allowed to receive payments from private companies. Also the pharmaceutical companies would not want their products run on a public network as someone could possibly decipher some of their secrets. In addition it would also probably breach the strict rules that apply to patents.


If that is true how is possible that RosettaLigand is used by private companies? What is relationship between resources provided by Rosetta and private research?


Rosetta is a software tool intended to aid in researching protein structures and can be used to help speed up the search for new drugs.

Rosetta@home is a project to improve the Rosetta software by using the spare processing power of home computers. None of the processing power you donate goes into private research.

The Rosetta software is freely available to academic and non-profit institutions but commercial organisations can use Rosetta if they pay a license fee. Revenue gained from licensing is reinvested into developing the Rosetta software.

Perhaps a useful analogy would be if you compared the Rosetta software to a test tube. We are all donating our computer power to develop a better form of test tube that can save time and money for researchers. Once the new test tube is designed, the maker of the test tube is giving out free test tubes to other universities and non-profit organisations. Some of these other organisations may be developing new drugs and will use the improved test tubes to further their research (saving time and money). Some or all of these non-profit organisations will be releasing their results into the public domain.

Continuing the test tube analogy, a private company also working in drug development wants to use the improved test tubes because they can save the company both time and money. The company pays the makers of the test tube a fee for the right to use them. The fee is pumped back directly into making an even better test tube. The company meanwhile uses the test tubes in their research. The company\'s end goal is to produce a drug to sell for a profit. They keep most of the details of their experiments a secret to protect their investment, but may be willing to release some data back to the test tube maker to help develop an even better test tube. Once a new drug has been found, the company markets it and sells it for a profit. If the new test tube was a success the company would have saved a lot of time and money, and may release the drug at a cheaper price than normal while still retaining their old profit margin.

Though the company does not disclose its research before the patent has been confirmed, the non-profit test tube maker has helped to reduce the costs of commercial drugs and perhaps allowed drugs to be developed years ahead of time, leading to many more lives saved.

So, BakerLab is working to improve the tool on a non-profit basis. And drug companies are working to use such tools to attack specific diseases/viruses etc. Read my prior comments on intellectual property rights here


Thanks for the link. If I understand it correctly RosettaLigand is available for anybody who wants to use it including pharmaceutical companies, but they have to use their own resources to run it and Rosetta does not do any computations for them?


The private company has to pay a license fee to use the Rosetta software which they then use on their private network. None of your computer time with Rosetta@home is used in their research.
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David Baker
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Message 60121 - Posted: 13 Mar 2009, 6:07:58 UTC - in response to Message 60107.  

I have a question regarding manuscript 3 from earlier this month. Mr. Baker describes RosettaLigand as very succesful in predicting pharmacologic interactions, but results are not public due to requirements of pharmaceutical companies using these predictions. I am questioning the information on home page of this project - Rosetta@home is not for profit. That was main reason I quit Predictor@home and started Rosetta. Is therefore possible that my computers were working on some results for private company that does not want to disclose the results now? I do not wish any of my machine work for private company. I pay for electricity and hardware, therefore any work for private companies should be optional with option not to participate.



I believe that it was said somewhere last year or so that the Baker Lab is not allowed to receive payments from private companies. Also the pharmaceutical companies would not want their products run on a public network as someone could possibly decipher some of their secrets. In addition it would also probably breach the strict rules that apply to patents.


YES! My lab is absolutely forbidden to receive payments from private companies! (you can read about Howard Hughes Medical Institute policies at their site). No work from rosetta@home has every been nor will ever be for a private company or for profit. in the case I referred to in my post, the company had a dataset that is useful for testing and comparing different ligand docking methods that has become a \"standard\" in the field. they do not profit from our test in any way, except indirectly (as the whole world does) insofar as it leads to the development of better drug design methods. the company, like any for-profit institution that wishes to use Rosetta must license the program from the UW (it is free for individuals and non profit instituations, but companies have to pay--this is how we support our annual developers meeting).

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Michael G.R.

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Message 60145 - Posted: 13 Mar 2009, 19:57:24 UTC
Last modified: 13 Mar 2009, 20:02:17 UTC

Thank you for the updates on the science the project is doing, Dr. Baker.

My main interest in Rosetta@home is so that we can help cure the diseases of aging (the #1 cause of death and suffering in the \"western\" world), either with a plan like Aubrey de Grey\'s SENS (see methuselahfoundation.org), or something else.

Work on fibrils (like in Alzheimer\'s) that accumulate as a toxic byproduct of simply being alive are a good step in that direction, as well as anything that makes gene therapy possible.

Keep up the good work, we\'ll keep crunching, and please keep updating us frequently.

Thanks!
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