David Baker\'s Rosetta@home journal

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David Baker
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Message 74065 - Posted: 21 Oct 2012, 5:47:09 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.
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Message 74200 - Posted: 8 Nov 2012, 4:23:35 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!

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Message 74231 - Posted: 10 Nov 2012, 2:18:24 UTC
Last modified: 10 Nov 2012, 2:42:08 UTC

We would like to acknowledge the Rosetta@Home participants who found the lowest energy structures for Nobu and Rie\'s designed proteins:

Fold-I : Aalelan (United States)
Fold-II : Jef (United States)
Fold-III : georgebg (Bulgaria)
Fold-IV: medvjet009(Czech Republic)
Fold-V : _2e_ Russia.

See Nobu\'s message board thread on \"Principles for designing ideal protein structures\" (http://boinc.bakerlab.org/rosetta/forum_thread.php?id=6113) for more information including a figure illustrating the critical role played by Rosetta@home in this work. And check out the latest on slashdot:
http://science.slashdot.org/story/12/11/09/020241/proteins-made-to-order
This and other publications from the lab are available at depts.washington.edu/bakerpg

Thanks again to everybody!!
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Message 74738 - Posted: 15 Dec 2012, 14:31:41 UTC

The CASP10 meeting just finished and all the results are on line so you can see what all your contributions made possible! Ray has posted a great summary of the results in the CASP10 thread on the science message boards. Overall, Rosetta@home was top or near top in most categories. I hate to embarrass David Kim who created RosettaHome and has kept it going, but his contact guided predictions were the highlight of CASP10 as they were vastly better than those of any other group. You can see this at
http://predictioncenter.org/casp10/results.cgi?view=targets&model=all&tr_type=others&groups_id=4
David\'s predictions are the black lines, those of other groups are in orange, better models stay below the rest of the pack.

Thanks to all of you who contributed to CASP10!!
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Message 75215 - Posted: 11 Mar 2013, 1:31:45 UTC

We have learned to design a new class of proteins which could be useful both as drugs and in sensors. As I\'ve explained before, most drugs are small molecules with fewer than 50 atoms. There are many drugs, such as blood thinning agents, which are very dangerous if given in too large doses. We have succeeded in designing proteins which bind to specific small molecules very tightly. These proteins could be used as antidotes in case of overdose with the target small molecule-for example we\'ve designed a protein which could be useful to treat toxicity due to overdose of the drug digoxin used to treat heart disease. With collaborators, we are working to use these designed proteins to detect levels of the target small molecules in the blood or in the environment.
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Message 75630 - Posted: 20 May 2013, 6:00:18 UTC

We have discovered how to make several new classes of protein structures! Rosetta@home has been absolutely critical in this work: when we design a sequence to fold into a new structure, the last thing we do before ordering a synthetic gene so we can make the protein in the laboratory is to send it out to you to predict the structure-if it folds to the structure we designed, we go ahead with it, but if you find that the lowest energy state is a different structure we go back to the drawing board. Our success rate in making brand new structures is far higher than I or anybody else ever expected, and the reason the success rate is so high is that your calculations provide a very stringent test of whether the designed sequence will actually fold the way it is supposed to. In the next few weeks I and other scientists here will describe to you the new classes of proteins we are making, and the many applications they will be useful for. Thank you for your absolutely essential contributions to this newly emerging scientific field!
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Message 76065 - Posted: 25 Sep 2013, 6:49:11 UTC

Our new Institute for Protein Design is making considerable progress as you can see at http://depts.washington.edu/ipd/. we are now using Rosetta@home to rigorously evaluate all computer-based designs before we create synthetic genes to make the proteins in the laboratory. this is dramatically increasing our success rate at designing proteins with new functions. your contributions continue to be absolutely invaluable!
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Message 76180 - Posted: 10 Nov 2013, 7:18:46 UTC

An article mentioning Rosetta@Home recently appeared in the Globe and Mail:

http://www.theglobeandmail.com/news/national/meet-two-pioneers-of-immune-research/article15101089/
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Message 76576 - Posted: 2 Apr 2014, 6:15:02 UTC

There has been very exciting recent progress in designing vaccines and small molecule binding proteins using Rosetta that is described in two recent papers in Nature. These and other recent advances are described in the new Rosetta@Home Research Updates thread. It was suggested there that we send out a monthly email newsletter describing recent progress--we haven\'t done this before to avoid clogging everybody\'s inboxes but we certainly could if there is interest.
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Message 76855 - Posted: 20 Jun 2014, 17:47:59 UTC

We have recently made great progress in designing self assembling materials from proteins and in designing proteins which selectively kill tumor cells. These efforts have benefited tremendously from Rosetta@Home! News releases on these advances are at
http://hsnewsbeat.uw.edu/story/self-assembling-nanomachines-start-click
http://hsnewsbeat.uw.edu/story/computer-designed-protein-causes-cancer-cells%E2%80%99-death
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Message 79421 - Posted: 18 Jan 2016, 5:46:32 UTC

We just published a paper in Nature that depended critically on all of your contributions! You can get the pdf for this paper on our website; you can also get pdfs of the many other papers we\'ve published in the last couple of years that relied heavily on rosetta@home. Here is the link to the recent Nature paper:

https://www.bakerlab.org/wp-content/uploads/2015/12/Brunette_Nature_2015.pdf
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Message 79521 - Posted: 12 Feb 2016, 6:38:13 UTC

The results on the flu neutralizing protein you helped us design have now been published. You can get the paper, like all of our papers, from our lab web site, and read what journalists are saying at

http://cen.acs.org/articles/94/i6/Designer-Protein-Promising-Antiflu-Agent.html
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Message 80192 - Posted: 17 Jun 2016, 6:32:20 UTC

I recommend listening to graduate student Yang Hsia\'s podcast on designing protein footballs which you can find on the Nature web site this week to go along with his paper. (see Ratika\'s post for the link if you can\'t find it). Thank you all again for all of your contributions to our research-we couldn\'t do it without you!
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Message 80456 - Posted: 1 Aug 2016, 5:02:31 UTC

We all collectively made the cover of the July 22nd Science-check it out! This same issue also has a news feature on our work, and an article on designed icosohedral cages made from two different designed protein building blocks. For more information and links to the papers, see Ratika\'s post in her thread.
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Message 80458 - Posted: 1 Aug 2016, 15:18:49 UTC

A link to \"Ratika\'s post\" for you, where you can also find links to a video explanation of the process.
Rosetta Moderator: Mod.Sense
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Message 81066 - Posted: 20 Jan 2017, 6:24:24 UTC

Hi Everybody!

this has been a good week with papers in this and last weeks Science magazine. your contributions were essential for both breakthroughs! here is some of the press you might find interesting:

http://www.geekwire.com/2017/big-data-rosetta-protein-puzzles/

https://www.theatlantic.com/science/archive/2017/01/unravelling-lifes-origami/513638/

http://www.geekwire.com/2017/uw-protein-pockets/

thank you again for your invaluable contributions to this research!!

David

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Message 81238 - Posted: 27 Feb 2017, 6:48:18 UTC
Last modified: 27 Feb 2017, 6:49:46 UTC

NOVA recently featured some of the work that all of you are contributing to:
http://www.pbs.org/wgbh/nova/physics/origami-revolution.html utm_medium=novasocial&utm_campaign=nova_2016&linkId=34331189 (the 8 minute segment on our work starts at 20:30)

The Economist also had an article on the work you are contributing to:
http://www.economist.com/news/science-and-technology/21716603-only-quarter-known-protein-structures-are-human-how-determine-proteins

Your contributions are highlighted particularly clearly in the Geekwire article:
http://www.geekwire.com/2017/big-data-rosetta-protein-puzzles/
which is titled \"Big data (and volunteers) help scientists solve hundreds of protein puzzles\"
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