Dr. Baker receives $10m+ grant for Rosetta HIV research!

Message boards : Number crunching : Dr. Baker receives $10m+ grant for Rosetta HIV research!

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Ethan
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Message 20681 - Posted: 20 Jul 2006, 0:52:32 UTC
Last modified: 20 Jul 2006, 3:45:07 UTC

The story doesn't really go into if it's solely for Baker's lab, but he is quoted in the article. I'm sure he'll be around to let us know more soon. In the mean time, CONGRATS!!!

http://seattlepi.nwsource.com/local/278100_aidsvaccine19ww.html

-Ethan
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Message 20691 - Posted: 20 Jul 2006, 3:49:42 UTC
Last modified: 20 Jul 2006, 3:50:26 UTC

Congratulations!
and keep working:)
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Message 20695 - Posted: 20 Jul 2006, 4:36:24 UTC

Well done and absolutly deserved! ;)
And just imagine what kind of computer-farm you could build with $10m... think of the RAC! :p
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Message 20707 - Posted: 20 Jul 2006, 8:23:50 UTC

Wow! Congratulations.....

I guess I won't have to scrape together mint stamps out of my collection to furnish to Feetfirst for the DVD mailings now. :-)

There we go. Reminds me of the scene in the movie, 'Contact', where Dr. Arraway was told, "You have your money".


Founder of BOINC GROUP - Objectivists - Philosophically minded rational data crunchers.


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Jose

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Message 20711 - Posted: 20 Jul 2006, 10:33:40 UTC

One of the elements that impress me the most about the announcement is the requirement that all the groups that are sharing the awards money MUST share information and collaborate with each other.

So not only is the grant a recognition of the great group of scientists that got funded but it is a call for more collaboration among scientists.

My only hope now is that David doenst go conventional on us and get a haircut. :)
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Message 20717 - Posted: 20 Jul 2006, 12:03:53 UTC

SELFISH POST AHEAD

I do have one concern. Will this project now expend more of its research solely for HIV or will cancer still be a big part of this project? Since I'm a cancer patient, I'm here to try to help others not to have to go through what I am going through. Will the lessons learned extend into the cancer research field?

tony
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Message 20729 - Posted: 20 Jul 2006, 15:40:56 UTC

I haven't seen details about how they intend to use Rosetta to fight cancer... but yes, if they learn how to "dock" with an selective portion of an HIV protein (the portion that doesn't constantly morph itself), they'll have another tool in the toolbox to apply to locating and knocking out cancer cells.

Actually, I believe their approach to HIV is to "design" a protein that looks similar enough to the unchanging portion of HIV that the body can build antibodies to it. So their current approach to HIV is, I believe, a vaccine. Not sure if the approach to cancer would be a vaccine or more of a drug, which would locate and dock with existing cancer cells and either genetically correct them back to normal, or prevent them from dividing.

Either way, "docking" or "design", the basic research Rosetta does can be applied to the proteins of other diseases.

...another way to look at it, if they are successful at creating an HIV vaccine, it would make it VERY easy to get sufficient funding to apply towards cancer research.

Hope your treatment is going well Tony.
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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/
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Profile Dimitris Hatzopoulos

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Message 20738 - Posted: 20 Jul 2006, 17:40:21 UTC

I think R's cancer-related approach was mostly focused on "gene therapy" kind of stuff, e.g. altering/creating DNA-modifying enzymes to repair damaged DNA

The other, "traditional" approach would be to help in "virtual screening" of drugs (like CureCancer approach) by

1/ identifying target proteins (protein structure prediction)
2/ "docking" (i.e. use Rosetta.exe instead of DOCK, AutoDOCK, THINK, LigandFit etc)
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Profile Keith E. Laidig
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Message 20739 - Posted: 20 Jul 2006, 17:59:00 UTC - in response to Message 20717.  

SELFISH POST AHEAD

I do have one concern. Will this project now expend more of its research solely for HIV or will cancer still be a big part of this project? Since I'm a cancer patient, I'm here to try to help others not to have to go through what I am going through. Will the lessons learned extend into the cancer research field?

tony


Tony,

For the foreseeable future the effort of R@H is actually cumulative in that what we learn on project A helps sharped the tools for project B as well.

Not only that, HIV is only a portion of the research effort here. Big $$$ for the entire project consortium to be sure, but we only get some. We've got irons in a number of fires and those won't get pushed aside just because Gates dumped some $$$ on the overall project.

On a personal note, here's hoping things go well for you. My family has been stricken by cancer.... I understand how tough it can be. -KEL

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Message 20744 - Posted: 20 Jul 2006, 18:43:08 UTC

I see it this way, (By the way Congrats Team Baker!!!) Bill Gates and Mr. Buffet just stuck a pencil in the eye of WSJ after their negative article concerning virtual microbiology experiments using DC. Also, If Rosetta and other DC's can produce tangible results to the HIV problem, then the gates are wide open for every single protein related desease problem. Things would really start to happen.

My opinion of Bill just went up a few points.

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Message 20790 - Posted: 21 Jul 2006, 3:46:30 UTC

AWESOME!
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Message 20797 - Posted: 21 Jul 2006, 6:31:12 UTC - in response to Message 20744.  

IAlso, If Rosetta and other DC's can produce tangible results to the HIV problem, then the gates are wide open for every single protein related desease problem. Things would really start to happen.

My opinion of Bill just went up a few points.



we feel the same way. the methods we are using to design potential HIV vaccines should be directly transferable to design of vaccines to other pathogens--basically, we design proteins that mimic critical regions on the pathogen to stimulate the immune system to make antibodies against these parts of the virus, bacteria, etc.

while we are very excited about making a serious push towards an HIV vaccine, this will not reduce our efforts to develop new proteins to target genes causing cancer. in fact, Jim Havranak in my group has just had very exciting results on engineering an endonuclease to cut within a human disease gene.
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Message 20818 - Posted: 21 Jul 2006, 13:07:07 UTC
Last modified: 21 Jul 2006, 13:22:37 UTC

In case Dr Baker's last comment "our efforts to develop new proteins to target genes causing cancer. in fact, Jim Havranak in my group has just had very exciting results on engineering an endonuclease to cut within a human disease gene." isn't quite clear for those of us who are not familiar with their science, here's a more elaborate description of Rosetta's recent work applicable to cancer (from 1-Jun-06 edition of Nature):


Protein engineering: OK Computer (pp 656-659)

One of the great remaining problems in computational protein design involves the redesign of a DNA-modifying protein so that it recognizes, and alters, a new DNA sequence. For example, changing the specificity of a nuclease a protein that cuts DNA at a specific site could be beneficial for a range of biotechnological and medical applications.
In this week's Nature, David Baker and colleagues have shown that it is possible to modify the sequence specificity of a "homing endonuclease" called I-MsoI. They used a computational approach to screen a virtual library of mutant proteins and predicted which amino acids needed to be changed to re-engineer this enzyme so that it recognized, and cleaved, a new DNA sequence. The mutant protein was highly active and was able to cleave the new DNA sequence, but did not modify the original sequence. The authors hope to redesign this and other DNA-modifying enzymes to alter a range of DNA sequences, so that they could specifically target almost any sequence in the genome. These computationally designed proteins may be useful in a range of medical and biotechnological applications, including gene therapeutic and other targeted genomics applications.

http://www.nature.com/nature/journal/v441/n7093/index.html

Nature Editor's Summary

1 June 2006
Design for living

Altering the specificity of DNA-cleaving enzymes could be useful in many medical or biotechnological applications, but it is quite a challenge in terms of computational protein design. Ashwell et al. have used computational redesign to alter the target-site specificity of the I-MsoI homing endonuclease, while maintaining wild-type binding affinity. The redesigned enzyme binds and cleaves the new DNA recognition site about 10,000 times more effectively than the wild-type enzyme, with target discrimination comparable to the original endonuclease. These results suggest that computational protein design methods can be used to create novel and highly specific endonucleases for gene therapy and other applications.
Letter: Computational redesign of endonuclease DNA binding and cleavage specificity

Justin Ashworth, James J. Havranek, Carlos M. Duarte, Django Sussman, Raymond J. Monnat, Jr, Barry L. Stoddard and David Baker

http://www.nature.com/nature/journal/v441/n7093/edsumm/e060601-14.html
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Message 20839 - Posted: 21 Jul 2006, 17:02:33 UTC
Last modified: 21 Jul 2006, 17:03:27 UTC

Dr. Baker:
I'd like to add my congratulations to you. Nicely done and well deserved.
It's nice to see the Gates Foundation get into this area.
I assume this means you can cut down the mac and cheese dinners to twice a week?
Sorry, I had to. <BG>
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Message 20867 - Posted: 22 Jul 2006, 8:56:28 UTC
Last modified: 22 Jul 2006, 9:00:08 UTC

My opinion of Bill just went up a few points.

Bill Gates is the worlds greatest philanthropist, these are grants made in the health sector alone so far this year!

A lot of the guys critics should read some of that site.

I would guess that the grant will be used to employ additional research staff, and support for them. I doubt there will be a reduction of emphasis on other areas because the grant was given for HIV research.

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.
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Message 21245 - Posted: 26 Jul 2006, 19:52:15 UTC - in response to Message 20867.  

The world would be a much better place if all the rich and powerfull like Gates would put their money for a better use...
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Message boards : Number crunching : Dr. Baker receives $10m+ grant for Rosetta HIV research!



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