DISCUSSION of Rosetta@home Journal (5)

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

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Sean Kiely

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Message 70370 - Posted: 18 May 2011, 20:03:11 UTC

Link to the paper that Dr. Baker mentions in his latest journal posting:

http://depts.washington.edu/bakerpg/drupal/system/files/windbichler11A.pdf
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Sid Celery

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Message 70371 - Posted: 19 May 2011, 1:17:15 UTC

Dr Baker:
Thanks for the recent updates and information on publications & papers. I find them very encouraging. I doubt I understood more than 3 or 4 words out of each 10 of the technical papers (often less) but the summaries & overviews provided here tell me it\'s geared toward important outcomes.

As much as you appreciate the userbase here, I wanted to say it\'s a privilege for me to be able to contribute to this work in whatever small way I do. Thanks for giving us the opportunity to do so.
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Michael G.R.

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Message 70629 - Posted: 23 Jun 2011, 19:22:02 UTC

I just want to say that I\'m EXTREMELY happy that R@H is working on amyloid fibril formations. Hopefully someday we have a vaccine!
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Sean Kiely

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Message 71295 - Posted: 19 Sep 2011, 17:26:18 UTC

Here\'s the link to the abstract of the article at nature.com that Dr. Baker discussed in his latest journal post:

http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.2119.html

Nature
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Aegis Maelstrom

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Message 71388 - Posted: 6 Oct 2011, 16:05:56 UTC

Great news regarding the \"excited state\" proteins.

Congratulations for the whole team and the crunching family!
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Sean Kiely

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Message 71481 - Posted: 24 Oct 2011, 16:19:19 UTC

Here\'s the link to the abstract of the \"Science\" article that Doctor Baker mentioned:

http://www.sciencemag.org/content/334/6054/373.abstract

Science


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Mad_Max

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Message 72207 - Posted: 23 Jan 2012, 21:22:54 UTC
Last modified: 23 Jan 2012, 21:23:48 UTC

I also want to describe a new research direction we are now embarking on aimed at future cancer therapies. There are a small set of proteins which are frequently found at much higher levels than normal on the surface of cancer cells. We are starting to design small proteins which bind tightly to these tumor cell markers. If we are successful, we have collaborators who will be testing these proteins for their ability to target cancer cell killing agents to the tumors.

And what is that set of proteins? They are not part of the immune system to detect (and / or kill) of defective cells?
If so, would not impact(by drugs/other protein) on these proteins also suppress work of the immune system?
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Message 72231 - Posted: 29 Jan 2012, 9:13:26 UTC

Last year we described in Science magazine the design of a new enzyme which catalyzes a chemical reaction called the Diels Alder reaction involving the formation of two carbon-carbon bonds. This reaction is interesting because no natural enzymes are known to catalyze the reaction. However, it wasn\'t a very good enzyme, and we asked FoldIt players to try to improve it. As described in Nature Biotechnology this month, remarkably FoldIt players were able to make the designed enzyme 20 times faster by inserting a completely new loop which helps the enzyme bind the chemicals it links together. The combination of Rosetta@Home and FoldIt is turning out to be powerful indeed for solving challenging problems in biomedicine!


That\'s great news! Is there any mileage in running the FoldIt enzyme on Rosetta? It sounds like brute force (i.e. R@H) is good for evolution and FoldIt for revolution (kinda like punctuated evolution in nature) - does that seem correct?
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Mod.Sense
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Message 72236 - Posted: 29 Jan 2012, 14:51:10 UTC

That\'s great news! Is there any mileage in running the FoldIt enzyme on Rosetta? It sounds like brute force (i.e. R@H) is good for evolution and FoldIt for revolution (kinda like punctuated evolution in nature) - does that seem correct?


I belive that is what Dr. Baker means when he says that the combination of the two is very powerful. As you say, the human Fold.it player is more likely to find revolutionary or intuitive designs, and then Rosetta@home can be used to further refine them and further explore the area around the new design idea.
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Sean Kiely

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Message 72251 - Posted: 31 Jan 2012, 20:45:04 UTC

Here\'s the link to the abstract for the article in Nature Biotechnology
that Dr.Baker references:


Nature
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David Baker
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Message 72289 - Posted: 13 Feb 2012, 5:52:46 UTC - in response to Message 72236.  

That\'s great news! Is there any mileage in running the FoldIt enzyme on Rosetta? It sounds like brute force (i.e. R@H) is good for evolution and FoldIt for revolution (kinda like punctuated evolution in nature) - does that seem correct?


I belive that is what Dr. Baker means when he says that the combination of the two is very powerful. As you say, the human Fold.it player is more likely to find revolutionary or intuitive designs, and then Rosetta@home can be used to further refine them and further explore the area around the new design idea.



Yes I think this is a good way to look at it. We are still trying to understand when and how to use FoldIt to get new ideas on how to approach a problem. One area we are focused on now is to design inhibitors to flu strains our existing designs don\'t already inhibit. we\'ve been using Rosetta@home extensively for this and have some very promising designs we will soon be testing. but we have the feeling that there are other possible ways to tackle the problem, and to explore these we will be releasing soon a set of FoldIt puzzles aimed at identifying other ways to grab onto the virus surface.
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Message 72632 - Posted: 31 Mar 2012, 8:46:13 UTC

I just read the latest post (http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#72628).
In that post we\'re urged to commit more CPU cycles and recruit new users. Both would be easier if Rosetta was less of a \"black box\". Tasks go out and results go in, there\'s nothing in between. I\'m thinking of; status of problems, maybe intermediate positive or negative results.
More feedback to the users would be helpful in getting us to do more for Rosetta, I think.
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Message 72639 - Posted: 2 Apr 2012, 0:13:50 UTC

I completely agree, whilst I understand the researchers and scientists are very busy doing their job it would be great to get feedback more often, it would also encourage more folks to join.

Folding@Home is doing a pretty good job in keeping their crunchers happy with info, Rosetta should be doing the same ..
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David Baker
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Message 72698 - Posted: 8 Apr 2012, 18:07:18 UTC

I apologize for the lack of feedback; we are all really busy with the research-but this is no excuse. I\'ve asked the scientists using rosetta@home in my group to each open a new thread describing the problem they are working on, intermediate results, etc so hopefully you will be getting a lot of feedback soon!
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Sean Kiely

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Message 72711 - Posted: 9 Apr 2012, 19:01:46 UTC

Here\'s the link to the abstract of the article that Dr. Baker referenced in his most recent journal post:

Nature Chemical Biology
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LanDroid

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Message 72895 - Posted: 26 Apr 2012, 15:14:45 UTC - in response to Message 72632.  
Last modified: 26 Apr 2012, 15:51:32 UTC

In the last two months we believe we have made quite a breakthrough in structure prediction, and are excited to test the new method in CASP10.

Please start a thread on the CASP10 Competition (you have them for CASP8 & 9) and provide ongoing updates on that. How are CASP9 test units going, will CASP10 WU\'s be issued starting May 1, details on some of the targets, etc. ???

CASP10 is Boinc Vs. Independent Labs! We need to support this and publicize it to Boinc Teams...

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edikl

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Message 72898 - Posted: 26 Apr 2012, 17:59:28 UTC - in response to Message 72895.  

In the last two months we believe we have made quite a breakthrough in structure prediction, and are excited to test the new method in CASP10.

Please start a thread on the CASP10 Competition (you have them for CASP8 & 9) and provide ongoing updates on that. How are CASP9 test units going, will CASP10 WU\'s be issued starting May 1, details on some of the targets, etc. ???

CASP10 is Boinc Vs. Independent Labs! We need to support this and publicize it to Boinc Teams...



I couldn\'t agree more :)
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Profile Ed and Harriet Griffith
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Message 72916 - Posted: 29 Apr 2012, 0:14:51 UTC

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!

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David Baker
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Message 72929 - Posted: 29 Apr 2012, 23:45:30 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!



Yes it will help tremendously-thanks!!
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Filipe

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Message 72999 - Posted: 5 May 2012, 21:37:21 UTC
Last modified: 5 May 2012, 21:50:03 UTC

We need your help though, we are now testing many aspects of the new approach and are seriously limited by available CPU cycles. There are now so many flu inhibitor design and structure prediction jobs queued up on Rosetta@Home that there is an eight day wait before they are getting sent out to you. This would be a great time to temporarily increase Rosetta@Home\'s share on your computers and/or recruit new users, we need all the help we can get! thanks



Rosetta@home have been approaching the 200 teraflops barrier,from an average of 120Tflps a few days ago.

It´s a quite nice improvement.
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Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (5)



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