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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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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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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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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Great news regarding the "excited state" proteins.

Congratulations for the whole team and the crunching family!

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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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?

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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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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Rosetta Moderator: Mod.Sense

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


Nature

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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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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 ..

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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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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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...

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 :)

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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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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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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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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